Inhibitors of cysteine proteases and methods of use thereof

ABSTRACT

The disclosure provides compounds, such as compounds of Formula II, with warheads and their use in treating medical diseases or disorders, such as viral infections. Pharmaceutical compositions and methods of making various compounds with warheads are provided. The compounds are contemplated to inhibit proteases, such as the 3C, CL- or 3CL-like protease.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. Ser. No. 17/665,204, filedFeb. 4, 2022, which is a continuation of U.S. Ser. No. 17/384,369, filedJul. 23, 2021, now U.S. Pat. No. 11,312,704, issued Apr. 26, 2022, whichis a continuation of U.S. Ser. No. 17/230,727, filed Apr. 14, 2021, nowU.S. Pat. No. 11,124,497, issued Sep. 21, 2021, which claims the benefitof, and priority to, U.S. Ser. No. 63/012,039 filed Apr. 17, 2020; U.S.Ser. No. 63/031,357 filed May 28, 2020; U.S. Ser. No. 63/036,866 filedJun. 9, 2020; U.S. Ser. No. 63/039,297 filed Jun. 15, 2020; U.S. Ser.No. 63/067,669 filed Aug. 19, 2020; U.S. Ser. No. 63/091,630 filed Oct.14, 2020; U.S. Ser. No. 63/129,018 filed Dec. 22, 2020; U.S. Ser. No.63/171,675 filed Apr. 7, 2021; U.S. Ser. No. 63/172,478 filed Apr. 8,2021; and U.S. Ser. No. 63/173,146 filed Apr. 9, 2021, the contents ofeach of which are incorporated herein by reference in their entirety.

BACKGROUND

The Coronaviridae family of viruses are enveloped, single-stranded,positive-sense RNA viruses and include 141 species that are classifiedinto four genera according to their phylogenetic relationships: α-, β-,γ-, and δ-coronavirus. Coronaviruses (CoVs) are zoonotic viruses thatinfect a variety of animals from whales to birds, bats, cats, andhumans. Typically, CoV infection results in mild to moderate respiratorytract infections; however, some CoV species are extremely virulent andcan result in widespread fatality. Severe acute respiratory syndromecoronavirus (SARS-CoV) is a human CoV that was responsible for the firstpandemic of the 21^(st) century, infecting over 8,000 people with a 10%mortality rate. Middle East respiratory syndrome coronavirus (MERS-CoV)was identified in November 2012 and had since infected over 1,600 peoplein 26 countries with 36% mortality rate. More recently, COVID-19 (SARSCoV2) coronaviruses have raised a global pandemic since they had beenfirst identified in China in late 2019. Therefore, it is important toidentify coronavirus drug targets that can be utilized for thedevelopment of broad-spectrum anti-coronaviral therapeutics to combatinfections of existing and emerging coronaviruses.

All CoVs express a >800 kDa replicase polyprotein that contains eithertwo or three cysteine proteases, the papain-like protease(s) (PLPpro, orPLP1 and PLP2) and the 3C-like protease (3CLpro, nsp5, or Mpro). Theseproteases process the CoV replicase polyprotein by cleaving it into 16non-structural proteins, which are responsible for a variety of aspectsof CoV replication. The CoV 3CLpro is responsible for processing 11cleavage sites of within the replicase polyprotein and is essential forCoV replication, making it a highly valuable target for therapeuticdevelopment. The overall active site architecture and substraterecognition pockets are structurally conserved across CoV 3CLpros,increasing its attractiveness as a target for the development ofbroad-spectrum anti-CoV therapeutics. Moreover, high sequenceconservation in the vicinity of active site among CoV 3CLpros fromdifferent coronavirus subclasses make them an excellent target for thedevelopment of broad-spectrum therapeutics for coronavirus infections.Accordingly, the development of CoV 3CLpro inhibitors is a promisingpath for the treatment of respiratory tract infections and relateddiseases.

Numerous studies on targeting the immediate zoonotic reservoirs ofcoronaviruses with small molecule inhibitors have helped informstructure-based design strategies aimed at creating molecular scaffoldsthat may aid in the development of therapeutic against coronaviralinfection; however, small molecule antiviral agents nor effectivecommercially available broad-spectrum therapeutics have not yet beenidentified. There is a critical need for the development ofbroad-spectrum CoV therapeutics to overcome the challenges oftraditional anti-CoV therapeutic development, as broad-spectrumtherapeutics can be rapidly implemented upon zoonotic disease outbreak.

SUMMARY

The disclosure is directed to, in part, viral protease inhibitors. Alsoprovided are pharmaceutical compositions comprising at least onedisclosed compound and a pharmaceutically acceptable carrier.

In an embodiment, provided herein is a viral protease inhibitor,comprising a warhead covalently bound to a 3C or 3CL protease inhibitor,wherein the antiviral compound covalently binds to Cys on the protease,and wherein the antiviral compound is active against one or moreviruses.

Also provided herein are compounds represented by Formula II:

wherein: R^(3a) is selected from

and 4-10 membered heterocycle, wherein the heterocycle may optionally besubstituted by one, two or three substituents each selected from thegroup consisting of hydroxyl, C₁-C₈alkoxy, oxo and a warhead A; R^(3b)is selected from hydrogen and C₁-C₈alkyl; wherein R³ and R^(3b) may bejoined together to form, together with the carbon to which they areattached, a 4-10 membered heterocycle, wherein the heterocycle mayoptionally be substituted by one, two or three substituents eachselected from C₆-C₁₄aryl and a warhead A; R^(1a) is selected from thegroup consisting of hydrogen, C₁-C₈alkyl, C₁-C₈heteroalkyl,—(C₁-C₈alkyl)-R¹, —(C₁-C₈alkyl)-CN, C₃-C₁₀cycloalkyl, C₆-C₁₄aryl, 4-10membered heterocycle and 5-10 membered heteroaryl; R^(1b) is selectedfrom hydrogen and C₁-C₈alkyl; or R^(1a) and R^(1b) may be joinedtogether to form, together with the carbon to which they are attached, a4-10 membered mono or bicyclic heterocycle having a ring nitrogen,NR^(G), or a C₃-C₁₀cycloalkyl; R¹ is selected from the group consistingof C₁-C₈alkyl, C₂-C₁₀alkenyl, C₂-C₁₀alkynyl, C₃-C₁₀cycloalkyl,C₆-C₁₄aryl, 5-10 membered heteroaryl and 4-10 membered heterocycle,wherein R¹ may optionally be substituted on a free carbon by one, two,or three substituents each selected from R^(A); R^(A) is independentlyselected, for each occurrence, halogen, cyano, hydroxyl, oxo, SF₅, CF₃,—O—CF₃, —O—CHF₂, —S—CH₃, —S(O)₂—CH₃, —NH₂, —O-phenyl,—O—(C₁-C₈alkyl)-phenyl, —NHC(O)R^(B), —NHC(O)OR^(B),—NHC(O)O—(C₁-C₈alkyl)-R^(B), —N(R^(y))₂,—N(R^(y))(C₁-C₈alkyl)C(O)O-phenyl, —N(R^(y))(C₁-C₈alkyl)C(O)N(R^(y))₂,—NHC(O)O(C₁-C₈alkyl)R^(B), —C(O)-(5-10 membered heteroaryl), —C(O)-(4-10membered heterocycle), —C(O)—O-(4-10 membered heterocycle),—C(O)—OC(CH₃)₃, —C(O)—(C₁-C₆alkyl), —C(O)—(C₂-C₁₀alkenyl)-(C₆-C₁₄aryl),C(O)—(C₁₋₆alkyl)-NHC(O)R^(B), —C₁-C₈alkyl, C₂-C₁₀alkenyl, C₂-C₁₀alkynyl,C₁-C₈heteroalkyl, C₁-C₈alkoxy, C₃-C₁₀cycloalkyl,—(C₁-C₈alkyl)-(C₃-C₁₀cycloalkyl), —(C₁-C₈alkyl)-(C₆-C₁₄aryl),—(C₁-C₈alkyl)-(5-10 membered heteroaryl), C₆-C₁₄aryl, 5-10 memberedheteroaryl and 4-10 membered heterocycle, wherein the R^(B),heterocycle, heteroaryl, or aryl may optionally be substituted by one,two or three substituents of halogen, C₁-C₈alkyl, C₁-C₈alkoxy, SF₅,—NH₂, hydroxyl or oxo; R² is selected from the group consisting of—NHC(O)R^(B), —NHC(O)N(R^(B))₂, —NHC(O)C(R^(C))₂R^(B), —NHS(O)₂R^(B),—O—(C₁-C₈alkyl)-(C₃-C₁₀cycloalkyl), 4-10 membered heterocycle,C₆-C₁₄aryl and 5-10 membered heteroaryl bound through the carbon ornitrogen atom, wherein R² may optionally be substituted by one, two, orthree substituents each selected from R^(x); or R^(1a) and R² may bejoined together to form, together with the carbon to which they areattached, a 4-10 membered mono or bicyclic heterocycle having a ringnitrogen NR^(G), or a C₃-C₁₀cycloalkyl, wherein the cycloalkyl orheterocycle may optionally be substituted by one, two or threesubstituents on a free carbon each selected from R^(A); R³ is selectedfrom 5-10 membered heteroaryl and 4-10 membered heterocycle, wherein R³may optionally be substituted by one, two, or three substituents eachselected from R^(A); R^(B) is independently selected, for eachoccurrence, from the group consisting of C₁-C₈alkyl (optionallysubstituted by one, two or three halo), C₂-C₁₀alkenyl, C₂-C₁₀alkynyl,C₆-C₁₄aryl, 5-10 membered heteroaryl and 4-10 membered heterocycle;R^(C) is independently selected, for each occurrence, from hydrogen,halogen and C₁-C₈alkyl; R^(x) is independently selected, for eachoccurrence, from the group consisting of halogen, hydroxyl, oxo, CF₃,SF₅, cyano, —OCHF₂, —OCF₃, —O—(C₁-C₈alkyl), —C(O)O(CH₃), —N(R^(y))₂,—N(R^(y))C(O)R^(y), —N(R^(y))(C₁-C₈alkyl)C(O)N(R^(y))₂,—N(R^(y))(C₁-C₈alkyl)C(O)OH, —(C₁-C₈alkyl)-(C₃-C₁₀cycloalkyl),C₁-C₈alkyl, C₁-C₈alkoxy, C₃-C₁₀cycloalkyl, C₆-C₁₄aryl, 5-10 memberedheteroaryl and 4-10 membered heterocycle, wherein the aryl, heterocycleor heteroaryl may optionally be substituted by one or more substituentseach selected from oxo, halogen and C₁-C₈alkyl; R^(G) is selected fromthe group consisting of H, C₁₋₆alkyl (optionally substituted by one, twoor three substituents each independently selected from the groupconsisting of —C(═O), halo, cyano, —NR^(m)R^(m), and —NH(C═O)R^(m)), andC(═O)—C₁₋₆-alkyl (optionally substituted by one, two or threesubstituents each independently selected from the group consisting ofhalo, cyano, —NR^(m)R^(m), —NR^(m)(C═O)R^(m), phenyl, cycloalkyl,heterocycle, C₁-C₆alkoxy, wherein R^(m) is selected for each occurrenceby H, C₁₋₃alkyl (optionally substituted by one, two or threesubstituents each independently selected from the group consisting ofhalo), phenyl (optionally substituted by halo), —S(O)₂—CH₃,C₃₋₆cycloalkyl, and 5-6 membered heteroaryl), —C(═O)—C₁₋₆alkyl(optionally substituted by one, two or three substituents eachindependently selected from the group consisting of halo, cyano andC₁-C₆alkoxy), C(═O)—C₃₋₆cycloalkyl, and C(═O)-(5-6 membered heteroaryl)(optionally substituted by halo, cyano, hydroxyl, NH₂, C₁₋₆alkyl,C₃₋₆cycloalkyl, C₁-C₆alkoxy, and C₁₋₆haloalkyl)); R^(y) is independentlyselected, for each occurrence, from the group consisting of hydrogen,C₁-C₈alkyl, C₁-C₈heteroalkyl, —CH₂CF₃, C₁-C₈alkoxy, —(C₁-C₈alkoxy)-(5-10membered aryl), C₃-C₆cycloalkyl and —(C₁-C₈alkyl)COOH; A is a warhead; Xis selected from the group consisting of C(R^(y)) and N, wherein R^(xy)is selected from the group consisting of H, D, —OH, —NH₂, halogen,C₁-C₈alkyl, C₁-C₈ haloalkyl, and C₁-C₈alkoxy; and pharmaceuticallyacceptable salts, stereoisomers, esters, and prodrugs thereof.

In some embodiments, provided herein are compounds represented byFormula II-A:

In some embodiments, provided herein are compounds represented byFormula II-B:

In some embodiments, provided herein are compounds represented byFormula II-I:

wherein: R³ is

R^(t) is independently, for each occurrence, H or methyl; or each R^(t)may be taken, together with the carbon to which they are attached, toform a cyclopropyl; R^(B) is selected from the group consisting of: a9-10 membered bicyclic heteroaryl having one ring nitrogen, C₁-C₆alkyl,and C₂-C₃alkenyl; wherein R^(B) is optionally substituted by one, two orthree substituents each independently selected from the group consistingof halogen, C₁-C₃alkoxy, NHR^(m), and phenyl (optionally substituted byone or two halogens); R^(m) is C₁₋₃alkyl or —C(O)—C₁₋₃alkyl, whereineach C₁₋₃alkyl is independently optionally substituted by one, two orthree halogens; or a pharmaceutically acceptable salt thereof.

In certain embodiments, provided herein are conjugates represented byFormula III:

wherein Cys₁₄₅ is cysteine at position 145 or equivalent active sitecysteine on a CL or 3CL protease; IR is a viral protease inhibitor; andwherein the compound that forms the conjugate comprises a —CN warhead.

DETAILED DESCRIPTION

The features and other details of the disclosure will now be moreparticularly described. Before further description of the presentdisclosure, certain terms employed in the specification, examples andappended claims are collected here. These definitions should be read inlight of the remainder of the disclosure and as understood by a personof skill in the art. Unless defined otherwise, all technical andscientific terms used herein have the same meaning as commonlyunderstood by a person of ordinary skill in the art.

Definitions

The term “treating” includes any effect, e.g., lessening, reducing,modulating, or eliminating, that results in the improvement of thecondition, disease, disorder and the like, including a reduction ofviral shedding in asymptomatic individuals and prophylaxis of exposedindividuals, independent of symptoms.

The term “alkyl” as used herein refers to a saturated straight orbranched hydrocarbon. Exemplary alkyl groups include, but are notlimited to, straight or branched hydrocarbons of 1-6, 1-4, or 1-3 carbonatoms, referred to herein as C₁₋₆alkyl, C₁₋₄alkyl, and C₁₋₃alkyl,respectively. Exemplary alkyl groups include, but are not limited to,methyl, ethyl, propyl, isopropyl, 2-methyl-1-butyl, 3-methyl-2-butyl,2-methyl-1-pentyl, 3-methyl-1-pentyl, 4-methyl-1-pentyl,2-methyl-2-pentyl, 3-methyl-2-pentyl, 4-methyl-2-pentyl,2,2-dimethyl-1-butyl, 3,3-dimethyl-1-butyl, 2-ethyl-1-butyl, butyl,isobutyl, t-butyl, pentyl, isopentyl, neopentyl, hexyl, etc.

The term “alkynyl” as used herein refers to an unsaturated straight orbranched hydrocarbon having at least one carbon-carbon triple bond.Exemplary alkynyl groups include, but are not limited to, straight orbranched groups of 2-6, or 3-6 carbon atoms, referred to herein asC₂₋₆alkynyl, and C₃₋₆alkynyl, respectively. Exemplary alkynyl groupsinclude, but are not limited to, ethynyl, propynyl, butynyl, pentynyl,hexynyl, methylpropynyl, etc.

The term “alkenyl” as used herein refers to an unsaturated straight orbranched hydrocarbon having at least one carbon-carbon double bond.Exemplary alkenyl groups include, but are not limited to, a straight orbranched group of 2-6 or 3-4 carbon atoms, referred to herein asC₁-C₈alkenyl, C₂-C₆alkenyl, and C₃-C₄alkenyl, respectively. Exemplaryalkenyl groups include, but are not limited to, vinyl, allyl, butenyl,pentenyl, etc.

The term “alkoxy” as used herein refers to a straight or branched alkylgroup attached to oxygen (alkyl-O—). Exemplary alkoxy groups include,but are not limited to, alkoxy groups of 1-6 or 2-6 carbon atoms,referred to herein as C₁-C₅alkoxy, C₁-C₆alkoxy, and C₂-C₆alkoxy,respectively. Exemplary alkoxy groups include, but are not limited tomethoxy, ethoxy, isopropoxy, etc.

The term “alkoxy” as used herein refers to a straight or branched alkylgroup attached to oxygen (alkyl-O—). Exemplary alkoxy groups include,but are not limited to, alkoxy groups of 1-6 or 2-6 carbon atoms,referred to herein as C₁-C₅alkoxy, C₁-C₆alkoxy, and C₂-C₆alkoxy,respectively. Exemplary alkoxy groups include, but are not limited tomethoxy, ethoxy, isopropoxy, etc.

The term “alkoxyalkyl” as used herein refers to a straight or branchedalkyl group attached to oxygen, attached to a second straight orbranched alkyl group (alkyl-O-alkyl-). Exemplary alkoxyalkyl groupsinclude, but are not limited to, alkoxyalkyl groups in which each of thealkyl groups independently contains 1-6 carbon atoms, referred to hereinas C₁₋₆alkoxy-C₁₋₆alkyl. Exemplary alkoxyalkyl groups include, but arenot limited to methoxymethyl, 2-methoxyethyl, 1-methoxyethyl,2-methoxypropyl, ethoxymethyl, 2-isopropoxyethyl etc.

The term “alkyoxycarbonyl” as used herein refers to a straight orbranched alkyl group attached to oxygen, attached to a carbonyl group(alkyl-O—C(O)—). Exemplary alkoxycarbonyl groups include, but are notlimited to, alkoxycarbonyl groups of 1-6 carbon atoms, referred toherein as C₁₋₆alkoxycarbonyl. Exemplary alkoxycarbonyl groups include,but are not limited to, methoxycarbonyl, ethoxycarbonyl,t-butoxycarbonyl, etc.

The term “alkenyloxy” used herein refers to a straight or branchedalkenyl group attached to oxygen (alkenyl-O—). Exemplary alkenyloxygroups include, but are not limited to, groups with an alkenyl group of3-6 carbon atoms, referred to herein as C₃₋₆alkenyloxy. Exemplary“alkenyloxy” groups include, but are not limited to allyloxy,butenyloxy, etc.

The term “alkynyloxy” used herein refers to a straight or branchedalkynyl group attached to oxygen (alkynyl-O). Exemplary alkynyloxygroups include, but are not limited to, groups with an alkynyl group of3-6 carbon atoms, referred to herein as C₃₋₆alkynyloxy. Exemplaryalkynyloxy groups include, but are not limited to, propynyloxy,butynyloxy, etc.

The term “aryl” refers to a radical of a monocyclic or polycyclic (e.g.,bicyclic or tricyclic) 4n+2 aromatic ring system (e.g., having 6, 10, or14 n electrons shared in a cyclic array) having 6-14 ring carbon atomsand zero heteroatoms provided in the aromatic ring system (“C₆₋₁₄aryl”). In some embodiments, an aryl group has six ring carbon atoms(“C₆ aryl”; e.g., phenyl). In some embodiments, an aryl group has tenring carbon atoms (“C₁₀ aryl”; e.g., naphthyl such as 1-naphthyl and2-naphthyl). In some embodiments, an aryl group has fourteen ring carbonatoms (“C₁₄ aryl”; e.g., anthracyl). “Aryl” also includes ring systemswherein the aryl ring, as defined above, is fused with one or morecarbocyclyl or heterocyclyl groups wherein the radical or point ofattachment is on the aryl ring, and in such instances, the number ofcarbon atoms continue to designate the number of carbon atoms in thearyl ring system. Typical aryl groups include, but are not limited to,groups derived from aceanthrylene, acenaphthylene, acephenanthrylene,anthracene, azulene, benzene, chrysene, coronene, fluoranthene,fluorene, hexacene, hexaphene, hexalene, as-indacene, s-indacene,indane, indene, naphthalene, octacene, octaphene, octalene, ovalene,penta-2,4-diene, pentacene, pentalene, pentaphene, perylene, phenalene,phenanthrene, picene, pleiadene, pyrene, pyranthrene, rubicene,triphenylene, and trinaphthalene. Particularly aryl groups includephenyl, naphthyl, indenyl, and tetrahydronaphthyl.

Examples of representative substituted aryls include the following

wherein one of R⁵⁶ and R⁵⁷ may be hydrogen and at least one of R⁵⁶ andR⁵⁷ is each independently selected from halogen, C₁-C₈ alkyl, C₁-C₈haloalkyl, 4-10 membered heterocyclyl, alkanoyl, C₁-C₈ alkoxy,heteroaryloxy, alkylamino, arylamino, heteroarylamino, NR⁵⁸COR⁵⁹,NR⁵⁸SOR⁵⁹NR⁵⁸SO₂R⁵⁹, COOalkyl, COOaryl, CONR⁵⁸R⁵⁹, CONR⁵⁸OR⁵⁹, NR⁵⁸R⁵⁹,SO₂NR⁵⁸R⁵⁹, S-alkyl, SOalkyl, SO₂alkyl, Saryl, SOaryl, SO₂aryl; or R⁵⁶and R⁵⁷ may be joined to form a cyclic ring (saturated or unsaturated)from 5 to 8 atoms, optionally containing one or more heteroatomsselected from the group consisting of N, O, and S. R⁶⁰ and R⁶¹ areindependently hydrogen, C₁-C₈ alkyl, C₁-C₄haloalkyl, C₃-C₁₀ cycloalkyl,4-10 membered heterocyclyl, C₆-C₁₀ aryl, substituted C₆-C₁₀ aryl, 5-10membered heteroaryl, or substituted 5-10 membered heteroaryl.

The term “carbonyl” as used herein refers to the radical —C(O)—.

The term “cyano” as used herein refers to the radical —CN.

The term “cycloalkoxy” as used herein refers to a cycloalkyl groupattached to oxygen (cycloalkyl-O—). Exemplary cycloalkoxy groupsinclude, but are not limited to, cycloalkoxy groups of 3-6 carbon atoms,referred to herein as C₃₋₆cycloalkoxy groups. Exemplary cycloalkoxygroups include, but are not limited to, cyclopropoxy, cyclobutoxy,cyclohexyloxy, etc.

The terms “cycloalkyl” or a “carbocyclic group” as used herein refers toa saturated or partially unsaturated hydrocarbon group of, for example,3-6, or 4-6 carbons, referred to herein as C₃-C₁₀cycloalkyl,C₃₋₆cycloalkyl or C₄₋₆cycloalkyl, respectively. Exemplary cycloalkylgroups include, but are not limited to, cyclohexyl, cyclopentyl,cyclopentenyl, cyclobutyl or cyclopropyl.

The terms “halo” or “halogen” as used herein refer to F, Cl, Br, or I.

The term “hetero” when used to describe a compound or a group present ona compound means that one or more carbon atoms in the compound or grouphave been replaced by a nitrogen, oxygen, or sulfur heteroatom. Heteromay be applied to any of the hydrocarbyl groups described above such asalkyl, e.g., heteroalkyl, cycloalkyl, e.g., heterocyclyl, aryl, e.g.,heteroaryl, cycloalkenyl, e.g., cycloheteroalkenyl, and the like havingfrom 1 to 5, and particularly from 1 to 3 heteroatoms.

The terms “heteroaryl” or “heteroaromatic group” as used herein refersto a monocyclic aromatic 5-10 membered ring system containing one ormore heteroatoms, for example one to three heteroatoms, such asnitrogen, oxygen, and sulfur. The term may also be used to refer to an8-10 membered bicyclic heteroaryl. Where possible, said heteroaryl ringmay be linked to the adjacent radical though carbon or nitrogen.Examples of heteroaryl rings include but are not limited to furan,thiophene, pyrrole, thiazole, oxazole, isothiazole, isoxazole,imidazole, pyrazole, triazole, pyridine or pyrimidine etc.

The terms “heterocyclyl,” “heterocycle,” or “heterocyclic group” areart-recognized and refer to saturated or partially unsaturated 4-10membered ring structures, whose ring structures include one to threeheteroatoms, such as nitrogen, oxygen, and sulfur. Where possible,heterocyclyl rings may be linked to the adjacent radical through carbonor nitrogen. The term may also be used to refer to 4-10 memberedsaturated or partially unsaturated ring structures that are bridged,fused or spirocyclic ring structures, whose ring structures include oneto three heteroatoms, such as nitrogen, oxygen, and sulfur. Examples ofheterocyclyl groups include, but are not limited to, pyrrolidine,piperidine, morpholine, thiomorpholine, piperazine, oxetane, azetidine,tetrahydrofuran or dihydrofuran etc. In some embodiments, theheterocycle is a spiro heterocycle (e.g. 2,8-diazaspiro[4.5]decane). Insome embodiments, the heterocycle is a bridged heterocycle (e.g.octahydro-1H-4,7-methanoisoindole). “Spiro heterocyclyl,” or “spiroheterocycle” refers to a polycyclic heterocyclyl with rings connectedthrough one common atom (called a spiro atom), wherein the rings haveone or more heteroatoms selected from the group consisting of N, O, andS(O)_(m) (wherein m is an integer of 0 to 2) as ring atoms.Representative examples of heterocyclyl include, for example:

The term “heterocyclyloxy” as used herein refers to a heterocyclyl groupattached to oxygen (heterocyclyl-O—).

The term “heteroaryloxy” as used herein refers to a heteroaryl groupattached to oxygen (heteroaryl-O—).

The terms “hydroxy” and “hydroxyl” as used herein refers to the radical—OH.

The term “oxo” as used herein refers to the radical ═O.

“Pharmaceutically or pharmacologically acceptable” include molecularentities and compositions that do not produce an adverse, allergic orother untoward reaction when administered to an animal, or a human, asappropriate. For human administration, preparations should meetsterility, pyrogenicity, and general safety and purity standards asrequired by FDA Office of Biologics standards.

The term “pharmaceutically acceptable carrier” or “pharmaceuticallyacceptable excipient” as used herein refers to any and all solvents,dispersion media, coatings, isotonic and absorption delaying agents, andthe like, that are compatible with pharmaceutical administration. Theuse of such media and agents for pharmaceutically active substances iswell-known in the art. The compositions may also contain other activecompounds providing supplemental, additional, or enhanced therapeuticfunctions.

The term “pharmaceutical composition” as used herein refers to acomposition comprising at least one compound as disclosed hereinformulated together with one or more pharmaceutically acceptablecarriers.

“Individual,” “patient,” or “subject” are used interchangeably andinclude any animal, including mammals, preferably mice, rats, otherrodents, rabbits, dogs, cats, swine, cattle, sheep, horses, or primates,and most preferably humans. The compounds of the disclosure can beadministered to a mammal, such as a human, but can also be administeredto other mammals such as an animal in need of veterinary treatment,e.g., domestic animals (e.g., dogs, cats, and the like), farm animals(e.g., cows, sheep, pigs, horses, and the like) and laboratory animals(e.g., rats, mice, guinea pigs, and the like). “Modulation” includesantagonism (e.g., inhibition), agonism, partial antagonism and/orpartial agonism.

In the present specification, the term “therapeutically effectiveamount” means the amount of the subject compound that will elicit thebiological or medical response of a tissue, system or animal, (e.g.mammal or human) that is being sought by the researcher, veterinarian,medical doctor or other clinician. The compounds of the disclosure areadministered in therapeutically effective amounts to treat a disease.Alternatively, a therapeutically effective amount of a compound is thequantity required to achieve a desired therapeutic and/or prophylacticeffect.

The term “pharmaceutically acceptable salt(s)” as used herein refers tosalts of acidic or basic groups that may be present in compounds used inthe compositions. Compounds included in the present compositions thatare basic in nature are capable of forming a wide variety of salts withvarious inorganic and organic acids. The acids that may be used toprepare pharmaceutically acceptable acid addition salts of such basiccompounds are those that form non-toxic acid addition salts, i.e., saltscontaining pharmacologically acceptable anions, including, but notlimited to, malate, oxalate, chloride, bromide, iodide, nitrate,sulfate, bisulfate, phosphate, acid phosphate, isonicotinate, acetate,lactate, salicylate, citrate, tartrate, oleate, tannate, pantothenate,bitartrate, ascorbate, succinate, maleate, gentisinate, fumarate,gluconate, glucaronate, saccharate, formate, benzoate, glutamate,methanesulfonate, ethanesulfonate, benzenesulfonate, p-toluenesulfonateand pamoate (i.e., 1,1′-methylene-bis-(2-hydroxy-3-naphthoate)) salts.Compounds included in the present compositions that are acidic in natureare capable of forming base salts with various pharmacologicallyacceptable cations. Examples of such salts include alkali metal oralkaline earth metal salts, particularly calcium, magnesium, sodium,lithium, zinc, potassium, and iron salts. Compounds included in thepresent compositions that include a basic or acidic moiety may also formpharmaceutically acceptable salts with various amino acids. Thecompounds of the disclosure may contain both acidic and basic groups;for example, one amino and one carboxylic acid group. In such a case,the compound can exist as an acid addition salt, a zwitterion, or a basesalt.

The compounds of the disclosure may contain one or more chiral centersand, therefore, exist as stereoisomers. The term “stereoisomers” whenused herein consist of all enantiomers or diastereomers. These compoundsmay be designated by the symbols “(+),” “(−),” “R” or “S,” depending onthe configuration of substituents around the stereogenic carbon atom,but the skilled artisan will recognize that a structure may denote achiral center implicitly. The present disclosure encompasses variousstereoisomers of these compounds and mixtures thereof. Mixtures ofenantiomers or diastereomers may be designated “(t)” in nomenclature,but the skilled artisan will recognize that a structure may denote achiral center implicitly.

The compounds of the disclosure may contain one or more double bondsand, therefore, exist as geometric isomers resulting from thearrangement of substituents around a carbon-carbon double bond. Thesymbol

denotes a bond that may be a single, double or triple bond as describedherein. Substituents around a carbon-carbon double bond are designatedas being in the “Z” or “E” configuration wherein the terms “Z” and “E”are used in accordance with IUPAC standards. Unless otherwise specified,structures depicting double bonds encompass both the “E” and “Z”isomers. Substituents around a carbon-carbon double bond alternativelycan be referred to as “cis” or “trans,” where “cis” representssubstituents on the same side of the double bond and “trans” representssubstituents on opposite sides of the double bond.

Compounds of the disclosure may contain a carbocyclic or heterocyclicring and therefore, exist as geometric isomers resulting from thearrangement of substituents around the ring. The arrangement ofsubstituents around a carbocyclic or heterocyclic ring are designated asbeing in the “Z” or “E” configuration wherein the terms “Z” and “E” areused in accordance with IUPAC standards. Unless otherwise specified,structures depicting carbocyclic or heterocyclic rings encompass both“Z” and “E” isomers. Substituents around a carbocyclic or heterocyclicrings may also be referred to as “cis” or “trans”, where the term “cis”represents substituents on the same side of the plane of the ring andthe term “trans” represents substituents on opposite sides of the planeof the ring. Mixtures of compounds wherein the substituents are disposedon both the same and opposite sides of plane of the ring are designated“cis/trans.”

Individual enantiomers and diastereomers of compounds of the presentdisclosure can be prepared synthetically from commercially availablestarting materials that contain asymmetric or stereogenic centers, or bypreparation of racemic mixtures followed by resolution methodswell-known to those of ordinary skill in the art. These methods ofresolution are exemplified by (1) attachment of a mixture of enantiomersto a chiral auxiliary, separation of the resulting mixture ofdiastereomers by recrystallization or chromatography and liberation ofthe optically pure product from the auxiliary, (2) salt formationemploying an optically active resolving agent, (3) direct separation ofthe mixture of optical enantiomers on chiral liquid chromatographiccolumns or (4) kinetic resolution using stereoselective chemical orenzymatic reagents. Racemic mixtures can also be resolved into theircomponent enantiomers by well-known methods, such as chiral-phase liquidchromatography or crystallizing the compound in a chiral solvent.Stereoselective syntheses, a chemical or enzymatic reaction in which asingle reactant forms an unequal mixture of stereoisomers during thecreation of a new stereocenter or during the transformation of apre-existing one, are well-known in the art. Stereoselective synthesesencompass both enantio- and diastereoselective transformations, and mayinvolve the use of chiral auxiliaries. For examples, see Carreira andKvaemo, Classics in Stereoselective Synthesis, Wiley-VCH: Weinheim,2009.

The compounds disclosed herein can exist in solvated as well asunsolvated forms with pharmaceutically acceptable solvents such aswater, ethanol, and the like, and it is intended that the disclosureembrace both solvated and unsolvated forms. In one embodiment, thecompound is amorphous. In one embodiment, the compound is a singlepolymorph. In another embodiment, the compound is a mixture ofpolymorphs. In another embodiment, the compound is in a crystallineform.

The disclosure also embraces isotopically labeled compounds of thedisclosure which are identical to those recited herein, except that oneor more atoms are replaced by an atom having an atomic mass or massnumber different from the atomic mass or mass number usually found innature. Examples of isotopes that can be incorporated into compounds ofthe disclosure include isotopes of hydrogen, carbon, nitrogen, oxygen,phosphorus, sulfur, fluorine and chlorine, such as ²H, ³H, ¹³C, ¹⁴C,¹⁵N, ¹⁸O, ¹⁷O, ³¹P, ³²P, ³⁵S, ¹⁸F, and ³⁶Cl, respectively. For example,a compound of the disclosure may have one or more H atom replaced withdeuterium.

Certain isotopically-labeled disclosed compounds (e.g., those labeledwith ³H and ¹⁴C) are useful in compound and/or substrate tissuedistribution assays. Tritiated (i.e., ³H) and carbon-14 (i.e., ¹⁴C)isotopes are particularly preferred for their ease of preparation anddetectability. Further, substitution with heavier isotopes such asdeuterium (i.e., ²H) may afford certain therapeutic advantages resultingfrom greater metabolic stability (e.g., increased in vivo half-life orreduced dosage requirements) and hence may be preferred in somecircumstances. Isotopically labeled compounds of the disclosure cangenerally be prepared by following procedures analogous to thosedisclosed in the examples herein by substituting an isotopically labeledreagent for a non-isotopically labeled reagent.

The term “prodrug” refers to compounds that are transformed in vivo toyield a disclosed compound or a pharmaceutically acceptable salt,hydrate or solvate of the compound. The transformation may occur byvarious mechanisms (such as by esterase, amidase, phosphatase, oxidativeand or reductive metabolism) in various locations (such as in theintestinal lumen or upon transit of the intestine, blood or liver).Prodrugs are well-known in the art (for example, see Rautio,Kumpulainen, et al, Nature Reviews Drug Discovery 2008, 7, 255). Forexample, if a compound of the disclosure or a pharmaceuticallyacceptable salt, hydrate or solvate of the compound contains acarboxylic acid functional group, a prodrug can comprise an ester formedby the replacement of the hydrogen atom of the acid group with a groupsuch as (C₁₋₈)alkyl, (C₂₋₁₂)alkylcarbonyloxymethyl,1-(alkylcarbonyloxy)ethyl having from 4 to 9 carbon atoms,1-methyl-1-(alkylcarbonyloxy)-ethyl having from 5 to 10 carbon atoms,alkoxycarbonyloxymethyl having from 3 to 6 carbon atoms,1-(alkoxycarbonyloxy)ethyl having from 4 to 7 carbon atoms,1-methyl-1-(alkoxycarbonyloxy)ethyl having from 5 to 8 carbon atoms,N-(alkoxycarbonyl)aminomethyl having from 3 to 9 carbon atoms,1-(N-(alkoxycarbonyl)amino)ethyl having from 4 to 10 carbon atoms,3-phthalidyl, 4-crotonolactonyl, gamma-butyrolacton-4-yl,di-N,N—(C₁₋₂)alkylamino(C₂₋₃)alkyl (such as β-dimethylaminoethyl),carbamoyl-(C₁₋₂)alkyl, N,N-di(C₁₋₂)alkylcarbamoyl-(C₁₋₂)alkyl andpiperidino-, pyrrolidino- or morpholino(C₂₋₃)alkyl.

Similarly, if a compound of the disclosure contains an alcoholfunctional group, a prodrug can be formed by the replacement of thehydrogen atom of the alcohol group with a group such as(C₁₋₆)alkylcarbonyloxymethyl, 1-((C₁₋₆)alkylcarbonyloxy)ethyl,1-methyl-1-((C₁₋₆)alkylcarbonyloxy)ethyl (C₁₋₆)alkoxycarbonyloxymethyl,N—(C₁₋₆)alkoxycarbonylaminomethyl, succinoyl, (C₁₋₆)alkylcarbonyl,α-amino(C₁₋₄)alkylcarbonyl, arylalkylcarbonyl and α-aminoalkylcarbonyl,or α-aminoalkylcarbonyl-α-aminoalkylcarbonyl, where eachα-aminoalkylcarbonyl group is independently selected from the naturallyoccurring L-amino acids, P(O)(OH)₂, —P(O)(O(C₁₋₆)alkyl)₂ or glycosyl(the radical resulting from the removal of a hydroxyl group of thehemiacetal form of a carbohydrate).

If a compound of the disclosure incorporates an amine functional group,a prodrug can be formed, for example, by creation of an amide orcarbamate, an N-alkylcarbonyloxyalkyl derivative, an(oxodioxolenyl)methyl derivative, an N-Mannich base, imine or enamine.In addition, a secondary amine can be metabolically cleaved to generatea bioactive primary amine, or a tertiary amine can metabolically cleavedto generate a bioactive primary or secondary amine. For examples, seeSimplfcio, et al., Molecules 2008, 13, 519 and references therein.

The term “warhead” or “warhead group” as used herein refers to afunctional group present on a compound wherein that functional group iscapable of reversibly or irreversibly participating in a reaction with aprotein, e.g., 3C or 3CL protease (e.g., with a cysteine on the proteasesuch as Cys 145). Warheads may, for example, form covalent bonds withthe protein, or may create stable transition states, or be a reversibleor an irreversible alkylating agent. For example, the warhead moiety canbe a functional group on an inhibitor that can participate in abond-forming reaction, wherein a new covalent bond is formed between aportion of the warhead and a donor, for example an amino acid residue ofa protein. In embodiments, the warhead is an electrophile and the“donor” is a nucleophile such as the side chain of a cysteine residue.As provided herein, a warhead may include a nitrile or halo group. Asalso provided herein, a warhead may include an aldehyde, ketoamides,hydroxybisulfite salts, heterocyclic moieties, aziridine, oxirane, epoxyketones, halomethyl ketones, hydroxymethyl ketones, electrophilicketones (e.g. trifluoromethyl ketones), acyloxymethyl ketones,benzothiazolyl ketones and a Michael acceptor. For example, nitriles maybe reversible covalent warheads for cysteine protease inhibition, forexample, where the mechanism of action may involve aformation ofreversible covalent bond between the nitrile and the active cysteine toform a thioimidate adduct. Reaction of cysteine of glutathione or otherproteins is generally reversible, while the reaction with cysteine oraminoethylthiols generally irreversibly forms a thiazolidine adduct. Itcan be appreciated that contemplated compounds herein may be areversible or an irreversible inhibitor.

Examples of exemplary warheads include, but not limited to, a moietywith a cyano, halomethyl, an aldehyde, ketoamide, hydroxybisulfite salt,heterocycle, epoxy ketone, halomethyl ketone, hydroxymethyl ketone,electrophilic ketone, acyloxymethyl ketone, benzothiazolyl ketone or aMichael acceptor, for example:

In some embodiments, the warhead is a moiety with a cyanohydrin orcyanoacrylate moiety. Examples of exemplary cyanohydrin andcyanoacrylate warheads include, but not limited to:

wherein R^(13bb) is selected from the group consisting of halogen,C₁-C₆alkyl, C₁-C₆haloalkyl, C₁-C₆alkoxy, C₃-C₁₀cycloalkyl,—N(R^(e)R^(f)), and —C(O)—N(R^(e)R^(f)); R^(e) and R^(f) are eachselected from the group consisting of hydrogen and C₁-C₆alkyl; or R^(e)and R^(f) may form, together with the nitrogen to which they areattached, a 4-6 membered heterocycle; and p is 0, 1, 2, 3, or 4, asvalency permits.

In some embodiments, the warhead is a moiety with a cyano amine or cyanoamide moiety. Examples of exemplary cyanoamine warheads include, but notlimited to:

wherein R^(13bb) is selected from the group consisting of halogen,C₁-C₆alkyl, C₁-C₆haloalkyl, C₁-C₆alkoxy, C₃-C₁₀cycloalkyl,—N(R^(e)R^(f)), and —C(O)—N(R^(e)R^(f)); R^(e) and R^(f) are eachselected from the group consisting of hydrogen and C₁-C₆alkyl; or R^(e)and R^(f) may form, together with the nitrogen to which they areattached, a 4-6 membered heterocycle; and p is 0, 1, 2, 3, or 4, asvalency permits.

In some embodiments, the warhead is a moiety with an imino-oxazolidinonemoiety. Examples of exemplary imino-oxazolidinone warheads include, butnot limited to:

In some embodiments, the warhead is a moiety with animinoimidazolidinone. Examples of exemplary iminoimidazolidinonewarheads include, but not limited to:

wherein each R^(ccc) and R^(ccc) is selected from the group consistingof hydrogen, C₁-C₈alkyl, C₃-C₆cycloalkyl, —(C₁-C₈alkyl)-(C₆-C₁₄aryl),and C₆-C₁₄aryl. In some embodiments, the warhead is selected from thegroup consisting of

Other examples of exemplary warheads include, but not limited to:

wherein R^(cc) is selected from the group consisting of hydrogen,C₁-C₈alkyl, C₃-C₆cycloalkyl, —(C₁-C₈alkyl)-(C₆-C₁₄aryl), C₆-C₁₄aryl,5-10 membered heteroaryl, —(C₁-C₈alkyl)-(5-10 membered heteroaryl), 5-10membered heterocycle and —N(R^(b)R^(c)), wherein R^(b) and R^(c) areeach selected from the group consisting of hydrogen, C₁-C₈alkyl, andC₃-C₆cycloalkyl, or R^(b) and R^(c) may be joined together to form,together with the nitrogen to which they are attached, a 5-10 memberedheterocycle.

Some other examples of exemplary warheads include, but not limited to:

wherein R^(cd) is selected from the group consisting of hydrogen,C₁-C₈alkyl, and C₃-C₆cycloalkyl.

Other examples of exemplary warheads include, but not limited to:

wherein R^(c) is selected from the group consisting of hydrogen,—CH₂C(O)O(C₁-C₈alkyl), C₁-C₈alkyl, and C₃-C₆cycloalkyl, wherein theC₁-C₈alkyl may optionally be substituted by one or more substituentseach selected from the group consisting of halogen, C₃-C₆cycloalkyl,5-10 membered aryl and 5-10 membered heteroaryl;

wherein X² is selected from the group consisting of NH, O and S; X³ isindependently selected, for each occurrence, from N and CH; R^(D) isindependently selected, for each occurrence, from the group consistingof C₁-C₈alkyl,

R^(E) is independently selected, for each occurrence, from the groupconsisting of halogen, hydroxyl, C₁-C₈alkyl and C₁-C₈alkoxy; p isselected from 0, 1 and 2; and q is selected from 0, 1 and 2;

wherein X² is selected from the group consisting of NH, NR^(P), O and S,wherein R^(P) is C₁-C₈alkyl; and

wherein R^(D) is selected from the group consisting of C₃-C₆cycloalkyl,C₁-C₈alkyl, and

X⁴ is independently selected, for each occurrence, from CH and N; R^(E)is independently selected, for each occurrence, from the groupconsisting of halogen, —CH₃, —OCH₃, —OCH₂CH₃, —OCH(CH₃)₂, —CN, —CF₃,—OCF₃ and —SCF₃; and p is selected from 0, 1 and 2; —C(O)R^(D), whereinR^(D) is selected from the group consisting of hydrogen, —CH₂OH, —CH₂OR′and —CH_(x)F_(y), wherein x is 0, 1 or 2; y is 1, 2 or 3; and the sum ofx and y is 3, wherein R is selected from the group consisting ofC₁-C₈alkyl, —(C₁-C₈alkyl)-(5-10 membered aryl), C₁-C₈heteroalkyl,C₃-C₆cycloalkyl and 5-10 membered aryl; and —(CH═CH)C(O)OR^(D), whereinR^(D) is C₁-C₈alkyl.

It will be appreciated to one of skilled in the art that the compoundsdisclosed herein that include the warheads above also contemplate theprecursors to those compounds, for example, where a cyano moietyinvolved in a warheads may be replaced with e.g., a halo moiety.

It will be appreciated to one of skilled in the art that the compoundsdisclosed herein can also irreversibly bind, or may otherwise inhibite.g., a virus protein via any other mechanism of action.

The term “inhibitor” as used herein refers to a compound that binds toand/or inhibits a target protease with measurable affinity.

The term “reversible” or “reversible inhibitor” as used herein refers toa protease inhibitor that associates with a protease in such a way as toinhibit the activity of the protease while the protease and inhibitorare bound, but does not associate with a protease in such a way as toinhibit the activity of the protease when the protease and inhibitor areno longer bound. Reversible inhibitors can effect inhibition bycompeting with substrate for binding to the active site of the protease(competitive reversible inhibitor), or by associating with the proteasebound to its substrate in a way to make the complex inactive(uncompetitive reversible inhibitor), or by associating with theprotease and/or protease-substrate complex in a way that inhibits theactivity of either and/or both.

As used herein, the term “irreversible” or “irreversible inhibitor”refers to an inhibitor (i.e. a compound) that is able to be covalentlybonded to a target protease in a substantially non-reversible manner. Anirreversible inhibitor will remain substantially bound to the targetprotease once covalent bond formation has occurred. Irreversibleinhibitors usually display time dependency, whereby the degree ofinhibition increases with the time with which the inhibitor is incontact with the enzyme. In certain embodiments, an irreversibleinhibitor will remain substantially bound to target protease oncecovalent bond formation has occurred and will remain bound for a timeperiod that is longer than the life of the protein.

I. Reversible or Irreversible Viral Protease Inhibitor Compounds

Also provided herein are compounds represented by

wherein: R^(3a) is selected from

and 4-10 membered heterocycle, wherein the heterocycle may optionally besubstituted by one, two or three substituents each selected from thegroup consisting of hydroxyl, C₁-C₈alkoxy, oxo and a warhead A; R^(3b)is selected from hydrogen and C₁-C₈alkyl; wherein R^(3a) and R^(3b) maybe joined together to form, together with the carbon to which they areattached, a 4-10 membered heterocycle, wherein the heterocycle mayoptionally be substituted by one, two or three substituents eachselected from C₆-C₁₄aryl and a warhead A; R^(1a) is selected from thegroup consisting of hydrogen, C₁-C₈alkyl, C₁-C₈heteroalkyl,—(C₁-C₈alkyl)-R¹, —(C₁-C₈alkyl)-CN, C₃-C₁₀cycloalkyl, C₆-C₁₄aryl, 4-10membered heterocycle and 5-10 membered heteroaryl; R^(1b) is selectedfrom hydrogen and C₁-C₈alkyl; or R^(1a) and R^(1b) may be joinedtogether to form, together with the carbon to which they are attached, a4-10 membered mono or bicyclic heterocycle having a ring nitrogen,NR^(G), or a C₃-C₁₀cycloalkyl; R¹ is selected from the group consistingof C₁-C₈alkyl, C₂-C₁₀alkenyl, C₂-C₁₀alkynyl, C₃-C₁₀cycloalkyl,C₆-C₁₄aryl, 5-10 membered heteroaryl and 4-10 membered heterocycle,wherein R¹ may optionally be substituted on a free carbon by one, two,or three substituents each selected from R^(A); R^(A) is independentlyselected, for each occurrence, halogen, cyano, hydroxyl, oxo, SF₅, CF₃,—O—CF₃, —O—CHF₂, —S—CH₃, —S(O)₂—CH₃, —NH₂, —O-phenyl,—O—(C₁-C₈alkyl)-phenyl, —NHC(O)R^(B), —NHC(O)OR^(B),—NHC(O)O—(C₁-C₈alkyl)-R^(B), —N(R^(y))₂,—N(R^(y))(C₁-C₈alkyl)C(O)O-phenyl, —N(R^(y))(C₁-C₈alkyl)C(O)N(R^(y))₂,—NHC(O)O(C₁-C₈alkyl)R^(B), —C(O)-(5-10 membered heteroaryl), —C(O)-(4-10membered heterocycle), —C(O)—O-(4-10 membered heterocycle),—C(O)—OC(CH₃)₃, —C(O)—(C₁-C₆alkyl), —C(O)—(C₂-C₁₀alkenyl)-(C₆-C₁₄aryl),C(O)—(C₁₋₆alkyl)-NHC(O)R^(B), —C₁-C₈alkyl, C₂-C₁₀alkenyl, C₂-C₁₀alkynyl,C₁-C₈heteroalkyl, C₁-C₈alkoxy, C₃-C₁₀cycloalkyl,—(C₁-C₈alkyl)-(C₃-C₁₀cycloalkyl), —(C₁-C₈alkyl)-(C₆-C₁₄aryl),—(C₁-C₈alkyl)-(5-10 membered heteroaryl), C₆-C₁₄aryl, 5-10 memberedheteroaryl and 4-10 membered heterocycle, wherein the R^(B),heterocycle, heteroaryl, or aryl may optionally be substituted by one,two or three substituents of halogen, C₁-C₈alkyl, C₁-C₈alkoxy, SF₅,—NH₂, hydroxyl or oxo; R² is selected from the group consisting of—NHC(O)R^(B), —NHC(O)N(R^(B))₂, —NHC(O)C(R^(C))₂R^(B), —NHS(O)₂R^(B),—O—(C₁-C₈alkyl)-(C₃-C₁₀cycloalkyl), 4-10 membered heterocycle,C₆-C₁₄aryl and 5-10 membered heteroaryl bound through the carbon ornitrogen atom, wherein R² may optionally be substituted by one, two, orthree substituents each selected from R^(x); or R^(1a) and R² may bejoined together to form, together with the carbon to which they areattached, a 4-10 membered mono or bicyclic heterocycle having a ringnitrogen NR^(G), or a C₃-C₁₀cycloalkyl, wherein the cycloalkyl orheterocycle may optionally be substituted by one, two or threesubstituents on a free carbon each selected from R^(A); R³ is selectedfrom 5-10 membered heteroaryl and 4-10 membered heterocycle, wherein R³may optionally be substituted by one, two, or three substituents eachselected from R^(A); R^(B) is independently selected, for eachoccurrence, from the group consisting of C₁-C₈alkyl (optionallysubstituted by one, two or three halo), C₂-C₁₀alkenyl, C₂-C₁₀alkynyl,C₆-C₁₄aryl, 5-10 membered heteroaryl and 4-10 membered heterocycle;R^(C) is independently selected, for each occurrence, from hydrogen,halogen and C₁-C₈alkyl; R^(x) is independently selected, for eachoccurrence, from the group consisting of halogen, hydroxyl, oxo, CF₃,SF₅, cyano, —OCHF₂, —OCF₃, —O—(C₁-C₈alkyl), —C(O)O(CH₃), —N(R^(y))₂,—N(R^(y))C(O)R^(y), —N(R^(y))(C₁-C₈alkyl)C(O)N(R^(y))₂,—N(R^(y))(C₁-C₈alkyl)C(O)OH, —(C₁-C₈alkyl)-(C₃-C₁₀cycloalkyl),C₁-C₈alkyl, C₁-C₈alkoxy, C₃-C₁₀cycloalkyl, C₆-C₁₄aryl, 5-10 memberedheteroaryl and 4-10 membered heterocycle, wherein the aryl, heterocycleor heteroaryl may optionally be substituted by one or more substituentseach selected from oxo, halogen and C₁-C₈alkyl; R^(G) is selected fromthe group consisting of H, C₁₋₆alkyl (optionally substituted by one, twoor three substituents each independently selected from the groupconsisting of —C(═O), halo, cyano, —NR^(m)R^(m), and —NH(C═O)R^(m)), andC(═O)—C₁₋₆-alkyl (optionally substituted by one, two or threesubstituents each independently selected from the group consisting ofhalo, cyano, —NR^(m)R^(m), —NR^(m)(C═O)R^(m), phenyl, cycloalkyl,heterocycle, C₁-C₆alkoxy, wherein R^(m) is selected for each occurrenceby H, C₁₋₃alkyl (optionally substituted by one, two or threesubstituents each independently selected from the group consisting ofhalo), phenyl (optionally substituted by halo), —S(O)₂—CH₃,C₃₋₆cycloalkyl, and 5-6 membered heteroaryl), —C(═O)—C₁₋₆alkyl(optionally substituted by one, two or three substituents eachindependently selected from the group consisting of halo, cyano andC₁-C₆alkoxy), C(═O)—C₃₋₆cycloalkyl, and C(═O)-(5-6 membered heteroaryl)(optionally substituted by halo, cyano, hydroxyl, NH₂, C₁₋₆alkyl,C₃₋₆cycloalkyl, C₁-C₆alkoxy, and C₁₋₆haloalkyl)); R^(y) is independentlyselected, for each occurrence, from the group consisting of hydrogen,C₁-C₈alkyl, C₁-C₈heteroalkyl, —CH₂CF₃, C₁-C₈alkoxy, —(C₁-C₈alkoxy)-(5-10membered aryl), C₃-C₆cycloalkyl and —(C₁-C₈alkyl)COOH; A is a warhead; Xis selected from the group consisting of C(R^(y)) and N, wherein R^(xy)is selected from the group consisting of H, D, —OH, —NH₂, halogen,C₁-C₈alkyl, C₁-C₈ haloalkyl, and C₁-C₈alkoxy; and pharmaceuticallyacceptable salts, stereoisomers, esters, and prodrugs thereof.

Also provided herein are compounds represented by

wherein R^(3a) is selected from

and 4-10 membered heterocycle, wherein the heterocycle may optionally besubstituted by one, two or three substituents each selected from thegroup consisting of hydroxyl, C₁-C₈alkoxy, oxo and a warhead A; R^(3b)is selected from hydrogen and C₁-C₈alkyl; wherein R^(3a) and R^(3b) maybe joined together to form, together with the carbon to which they areattached, a 4-10 membered heterocycle, wherein the heterocycle mayoptionally be substituted by one, two or three substituents eachselected from C₆-C₁₄aryl and a warhead A; R^(1a) is selected from thegroup consisting of C₁-C₈alkyl, —(C₁-C₈alkyl)-R¹, —(C₁-C₈alkyl)-CN,C₃-C₁₀cycloalkyl, C₆-C₁₄aryl, 4-10 membered heterocycle and 5-10membered heteroaryl; R^(1b) is selected from hydrogen and C₁-C₈alkyl;R^(1a) and R^(1b) may be joined together to form, together with thecarbon to which they are attached, a 4-10 membered heterocycle or aC₃-C₁₀cycloalkyl; R¹ is selected from the group consisting ofC₁-C₈alkyl, C₂-C₁₀alkenyl, C₂-C₁₀alkynyl, C₃-C₁₀cycloalkyl, C₆-C₁₄aryl,5-10 membered heteroaryl and 4-10 membered heterocycle, wherein R¹ mayoptionally be substituted by one, two, or three substituents eachselected from R^(A); R^(A) is independently selected, for eachoccurrence, halogen, cyano, hydroxyl, oxo, SF₅, —NH₂, —O-phenyl,—O—(C₁-C₈alkyl)-phenyl, —C(O)-(5-10 membered heteroaryl), —C(O)-(4-10membered heterocycle), —C(O)—O-(4-10 membered heterocycle),—C(O)—OC(CH₃)₃, —C(O)—(C₂-C₁₀alkenyl)-(C₆-C₁₄aryl) C₁-C₈alkyl,C₂-C₁₀alkenyl, C₂-C₁₀alkynyl, C₁-C₈heteroalkyl, C₁-C₈alkoxy,C₃-C₁₀cycloalkyl, —(C₁-C₈alkyl)-(C₆-C₁₄aryl), —(C₁-C₈alkyl)-(5-10membered heteroaryl), C₆-C₁₄aryl, 5-10 membered heteroaryl and 4-10membered heterocycle, wherein the heterocycle, heteroaryl, or aryl mayoptionally be substituted by one, two or three substituents of halogen,C₁-C₈alkyl, C₁-C₈alkoxy, SF₅, —NH₂, hydroxyl or oxo; R² is selected fromthe group consisting of —NHC(O)R^(B), —NHC(O)N(R^(B))₂,—NHC(O)C(R^(C))₂R^(B), —NHS(O)₂R^(B), 4-10 membered heterocycle,C₆-C₁₄aryl and 5-10 membered heteroaryl bound through the carbon ornitrogen atom, wherein R² may optionally be substituted by one, two, orthree substituents each selected from R^(x); R^(1a) and R² may be joinedtogether to form, together with the carbon to which they are attached, a4-10 membered heterocycle or a C₃-C₁₀cycloalkyl, wherein the cycloalkylor heterocycle may optionally be substituted by one, two or threesubstituents each selected from R^(A); R³ is selected from 5-10 memberedheteroaryl and 4-10 membered heterocycle, wherein R³ may optionally besubstituted by one, two, or three substituents each selected from R^(A);R^(B) is independently selected, for each occurrence, from the groupconsisting of C₁-C₈alkyl, C₂-C₁₀alkenyl, C₂-C₁₀alkynyl, C₆-C₁₄aryl, 5-10membered heteroaryl and 4-10 membered heterocycle; R^(C) isindependently selected, for each occurrence, from hydrogen andC₁-C₈alkyl; R^(x) is independently selected, for each occurrence, fromthe group consisting of halogen, hydroxyl, oxo, SF₅, cyano, —C(O)O(CH₃),—N(R^(y))₂, —N(R^(y))C(O)R^(y), C₁-C₈alkyl, C₁-C₈alkoxy,C₃-C₁₀cycloalkyl, C₆-C₁₄aryl, 5-10 membered heteroaryl and 4-10 memberedheterocycle, wherein the aryl, heterocycle or heteroaryl may optionallybe substituted by one or more substituents each selected from oxo andC₁-C₈alkyl; R^(y) is independently selected, for each occurrence, fromthe group consisting of hydrogen, C₁-C₈alkyl, C₁-C₈alkoxy,—(C₁-C₈alkoxy)-(5-10 membered aryl) and C₃-C₆cycloalkyl; A is a warhead;X is selected from CH, C(CH₃) and N; and pharmaceutically acceptablesalts, stereoisomers, esters, and prodrugs thereof.

In certain embodiments, the present disclosure provides compounds ofFormula II-A:

In certain embodiments, the present disclosure provides compounds ofFormula II-B:

In various embodiments, the present disclosure provides compounds ofFormula II-C:

In various embodiments, the present disclosure provides compounds ofFormula II-D-I or Formula II-D-II:

wherein pp is selected from 0, 1, 2, and 3.

In various embodiments, the present disclosure provides compounds ofFormula II-E:

wherein ss is selected from 0, 1, 2, and 3, and mm is selected from 1,2, and 3.

In some embodiments, provided herein are compounds represented byFormula II-I:

wherein: R³ is

R^(t) is independently, for each occurrence, H or methyl; or each R^(t)may be taken, together with the carbon to which they are attached, toform a cyclopropyl; R^(B) is selected from the group consisting of: a9-10 membered bicyclic heteroaryl having one ring nitrogen, C₁-C₆alkyl,and C₂-C₃alkenyl; wherein R^(B) is optionally substituted by one, two orthree substituents each independently selected from the group consistingof halogen, C₁-C₃alkoxy, NHR^(m), and phenyl (optionally substituted byone or two halogens); R^(m) is C₁₋₃alkyl or —C(O)—C₁₋₃alkyl, whereineach C₁₋₃alkyl is independently optionally substituted by one, two orthree halogens; or a pharmaceutically acceptable salt thereof.

In certain embodiments, R^(3a) is

wherein R^(xy) is selected from the group consisting of H, D, OH, NH₂,halogen, C₁-C₈alkyl, C₁-C₈ haloalkyl, and C₁-C₈alkoxy. In embodiments,R^(xy) is selected from the group consisting of H, D, CH₃, CH₂CH₃, F,and CF₃. In some embodiments, R^(xy) is F. In some embodiments, R^(xy)is CF₃. In some embodiments, CH₃. In some embodiments, R^(xy) is H.

In various embodiments, X is selected from the group consisting of CH,CD, C(CH₃), C(CH₂CH₃), N, CF, CCl, CBr, C(CHF₂), C(CH₂F), and C(CF₃). Insome embodiments, X is CH. In some embodiments, X is CD. In someembodiments, X is C(CH₃). In some embodiments, X is C(CF₃). In someembodiments, X is CF. In some embodiments, X is N.

In some embodiments, A is selected from the group consisting of cyano,—C(O)R^(D), —C(O)CH₂N(R^(b)R^(c)), —C(O)CH₂OC(O)R^(D), —C(O)C(O)R^(D),—(CH═CH)C(O)OR^(D), —(CH═CCN)C(O)OR^(D), —(CH═CCN)C(O)(NH)R^(D),—CH(CN)(OH), —CH(CN)(NR^(b)R^(c)),

wherein R^(D) is selected from the group consisting of hydrogen,hydroxyl, —OR^(bb)—N(R^(b)R^(c)), C₁-C₈alkyl, C₁-C₈alkoxy,C₃-C₆cycloalkyl, C₆-C₁₄aryl, 5-10 membered heteroaryl, and 4-10 memberedheterocycle; wherein R^(D) may optionally be substituted by one, two, orthree substituents each selected from the group consisting of halogen,hydroxyl, and R^(E); R^(E) is selected from the group consisting ofC₁-C₈alkyl, C₁-C₈alkoxy, C₆-C₁₄aryl, 4-10 membered heterocycle, and 5-10membered heteroaryl, wherein R^(E) may optionally be substituted by one,two, or three substituents each selected from halogen, cyano, C₁-C₈alkyland C₁-C₈alkoxy; R^(bb) is selected from the group consisting ofC₃-C₆cycloalkyl, C₆-C₁₄aryl, —(C₁-C₈alkyl)-C₆-C₁₄aryl, 5-10 memberedheteroaryl, and 4-10 membered heterocycle; R^(cc) is selected from thegroup consisting of hydrogen, C₁-C₈alkyl, C₃-C₆cycloalkyl,—(C₁-C₈alkyl)-(C₆-C₁₄aryl), C₆-C₁₄aryl, 5-10 membered heteroaryl,—(C₁-C₈alkyl)-(5-10 membered heteroaryl), 5-10 membered heterocycle and—N(R^(b)R^(c)), wherein R^(b) and R^(C) are each selected from the groupconsisting of hydrogen, C1-C₈alkyl, and C₃-C₆cycloalkyl, or R^(b) andR^(c) may be joined together to form, together with the nitrogen towhich they are attached, a 5-10 membered heterocycle; R^(cd) is selectedfrom the group consisting of hydrogen, C₁-C₈alkyl, and C₃-C₆cycloalkyl;and R^(b) and R^(C) are each selected from the group consisting ofhydrogen, —CH₂C(O)O(C₁-C₈alkyl), —C(O)—(C₁-C₈alkyl),—S(O)₂—(C₁-C₈alkyl), C₁-C₈alkyl, C₃-C₆cycloalkyl and—(C₁-C₈alkyl)-C₆-C₁₄aryl, wherein the C₁-C₈alkyl may optionally besubstituted by one or more substituents each selected from the groupconsisting of halogen, C₃-C₆cycloalkyl, C₆-C₁₄aryl, 4-10 memberedheterocycle, and 5-10 memberedIn embodiments, A is selected from the group consisting of —CN,

In embodiments, R^(1a) is selected from the group consisting of

In embodiments, R^(1a) is —(C₁-C₈alkyl)-R¹.

In embodiments, R^(1b) is hydrogen.

In certain embodiments, R^(1a) and R^(1b) are joined to together to form

In certain embodiments, R^(3a) is a 4-10 membered heterocycle.

In some embodiments, R^(3a) is selected from the group consisting of

In some embodiments, R³ is a 4-10 membered heterocycle.

In some embodiments, R³ is selected from

In some embodiments, R³ is

(for example,

wherein R^(x3) are independently for each occurrence selected from thegroup consisting of hydrogen, halogen, C₁-C₈alkyl, C₁-C₈ haloalkyl,C₃-C₆cycloalkyl, and C₁-C₈alkoxy; and pp is selected from 0, 1, 2, and3. In some embodiments, R³ is

In some embodiments, R³ is

In some embodiments, R³ is

In some embodiments, R³ is

In some embodiments, R³ is

and R^(t) is independently, for each occurrence, H or methyl; or eachR^(t) may be taken, together with the carbon to which they are attached,to form a cyclopropyl.

In some embodiments, R³ is selected from the group consisting of

In some embodiments, wherein R³ is selected from the group consisting of

In some embodiments, wherein R³ is selected from the group consisting of

In some embodiments, R² is selected from the group consisting of

In some embodiments, R^(1a) and R² are joined to together to form theheterocycle selected from the group consisting of:

In some embodiments, R^(1a) and R² are joined to together to form theheterocycle selected from the group consisting of:

and R^(1b) is H.

In some embodiments, R^(1a) and R² are joined to together to form theheterocycle selected from the group consisting of:

and R^(1b) is H.

In some embodiments, R^(1a) and R² are joined to together to form theheterocycle selected from the group consisting of:

and R^(1b) is H.

In some embodiments, R^(G) is selected from the group consisting of H,C₁₋₆alkyl (optionally substituted by one, two or three substituents eachindependently selected from the group consisting of —C(═O), halo, cyano,—NR^(m)R^(m), and —NH(C═O)R^(m)) and C(═O)—C₁₋₆alkyl (optionallysubstituted by one, two or three substituents each independentlyselected from the group consisting of halo, cyano, —NR^(m)R^(m),—NR^(m)(C═O)R^(m), phenyl, cycloalkyl and heterocycle, wherein R^(m) isselected for each occurrence by H or C₁₋₃alkyl (optionally substitutedby one, two or three halogens, e.g., F), or C₃-C₆cycloalkyl (optionallysubstituted by one, two, or three F).

In some embodiments, R^(G) is selected from the group consisting of

In some embodiments, R^(G) is

In some embodiments, the compound is represented by

e.g.,

wherein R^(G3) is selected from the group consisting of H, C₁₋₆alkyl,C₃₋₆cycloalkyl (e.g., t-butyl, propyl, cyclopropyl), phenyl andheterocycle; and R^(G2) is —NH(C═O)R^(m), wherein R^(m) is selected foreach occurrence by H, methyl or CF₃.

In some embodiments, the compound is represented by

wherein R^(G3) is selected from the group consisting of H, C₁₋₆alkyl,C₃₋₆cycloalkyl, phenyl and heterocycle; and R^(G2) is —NH(C═O)R^(m),wherein R^(m) is selected for each occurrence by H, methyl or CF₃.

In some embodiments, the compound is represented by

wherein R^(G3) is selected from the group consisting of H, C₁₋₆alkyl,C₃₋₆cycloalkyl, phenyl and heterocycle; and R^(G2) is —NH(C═O)R^(m),wherein R^(m) is selected for each occurrence by H, methyl or CF₃.

In some embodiments, the compound is represented by

wherein R^(G3) is selected from the group consisting of H, C₁₋₆alkyl(optionally substituted by one, two or three C₁-C₆alkoxy),C₃₋₆cycloalkyl, phenyl and heterocycle; and R^(G2) is selected from thegroup consisting of —NH(C₁₋₃alkyl) (optionally substituted by one, twoor three substituents each independently selected from the groupconsisting of halo, optionally substituted phenyl, —S(O)₂—CH₃,C₃₋₆cycloalkyl, and 5-6 membered heteroaryl) and —NH(C═O)R^(m), whereinR^(m) is selected for each occurrence by H, C₁₋₆alkyl (optionallysubstituted by one, two or three substituents each independentlyselected from the group consisting of halo, cyano and C₁-C₆alkoxy),CHF₂, CF₃, or 5-6 membered heteroaryl (optionally substituted by halo,cyano, hydroxyl, NH₂, C₁₋₆alkyl, C₃₋₆cycloalkyl, C₁-C₆alkoxy, CHF₂, andCF₃).

In some embodiments, the compound is represented by

wherein R^(G3) is selected from the group consisting of H, C₁₋₆alkyl(optionally substituted by one, two or three C₁-C₆alkoxy),C₃₋₆cycloalkyl, phenyl and heterocycle; and R^(G2) is selected from thegroup consisting of —NH(C₁₋₃alkyl) (optionally substituted by one, twoor three substituents each independently selected from the groupconsisting of halo, optionally substituted phenyl, —S(O)₂—CH₃,C₃₋₆cycloalkyl, and 5-6 membered heteroaryl) and —NH(C═O)R^(m), whereinR^(m) is selected for each occurrence by H, C₁₋₆alkyl (optionallysubstituted by one, two or three substituents each independentlyselected from the group consisting of halo, cyano and C₁-C₆alkoxy),CHF₂, CF₃, or 5-6 membered heteroaryl (optionally substituted by halo,cyano, hydroxyl, NH₂, C₁₋₆alkyl, C₃₋₆cycloalkyl, C₁-C₆alkoxy, CHF₂, andCF₃).

In some embodiments, R^(G3) is selected from the group consisting of

In some embodiments, R^(G2) is selected from the group consisting of

wherein R^(F) is selected from the group consisting of C₁₋₆alkyl,C₃₋₆cycloalkyl, phenyl and 5-6 membered heteroaryl, wherein R^(F) mayoptionally be substituted by one, two or three substituents selectedfrom the group consisting of halo, cyano, hydroxyl and C₁-C₆alkoxy; andX^(F) is selected from the group consisting of H, halo, cyano, hydroxyl,NH₂, C₁₋₆alkyl, C₃₋₆cycloalkyl, C₁-C₆alkoxy, and C₁₋₆haloalkyl.

In some embodiments, R^(1a) and R² are joined to together to form theheterocycle selected from the group consisting of:

In some embodiments, the compound is selected from the group consistingof the compounds identified in Table 1 below:

TABLE 1 Exemplary compounds. Com- pound No. Structure 100

101

102

103

104

105

106

107

108

109

110

111

112

113

114

115

116

117

118

119

120

121

122

123

124

125

126

127

128

129

130

131

132

133

134

135

136

137

138

139

140

141

142

143

144

145

146

147

148

149

150

151

152

153

154

155

156

157

158

159

160

161

162

163

164

165

166

167

168

169

170

171

172

173

174

175

176

177

178

179

180

181

182

183

184

185

186

187

188

189

190

191

196

197

198

199

200

201

202

203

204

205

206

207

208

209

210

211

212

213

214

215

216

217

218

219

220

221

222

223

224

225

226

227

230

231

232

233

234

235

236

237

238

239

240

241

242

243

244

245

246

247

248

249

250

251

252

253

254

255

256

257

258

259

260

261

262

263

264

265

266

267

268

269

270

271

272

273

274

275

276

277

278

279

280

281

282

283

284

285

286

287

288

289

290

291

292

293

294

295

296

297

298

299

300

301

302

303

304

305

306

307

308

309

310

311

312

313

314

315

316

317

318

319

320

321

322

323

324

325

326

327

328

329

330

331

332

333

334

335

336

337

338

339

340

341

342

343

344

345

346

347

348

349

350

351

352

353

354

355

356

357

358

359

360

361

362

363

364

365

366

367

368

369

370

371

372

373

374

375

376

377

378

379

380

381

382

383

384

385

386

387

388

389

390

391

392

393

394

395

396

397

398

399

400

401

402

403

404

405

406

407

408

409

410

411

412

413

414

415

416

417

418

419

420

421

422

423

424

425

426

427

428

429

430

431

432

433

434

435

436

437

438

439

440

441

442

443

444

445

446

447

448

449

450

451

452

453

454

455

456

457

458

459

460

461

462

463

464

465

466

467

468

469

470

471

472

473

474

475

476

477

478

479

480

481

482

483

484

485

486

487

488

489

490

491

492

493

494

495

496

497

498

499

500

501

502

503

504

505

506

507

508

509

510

511

512

513

514

515

516

517

518

519

520

521

522

523

524

525

526

527

528

529

530

531

532

533

534

535

536

537

538

539

540

541

542

543

544

545

546

547

548

549

550

551

552

553

554

555

556

557

558

559

560

561

562

563

564

565

566

567

568

569

570

571

572

573

574

575

576

577

578

579

580

581

582

583

584

585

586

587

588

589

590

591

592

593

594

595

596

597

598

599A

599

600A

600

601A

601

344A

344B

344C

344D

602A

602

603

604

605

606

607

608

609

610

611

612

613

614

615

616

617

618

619

620

621

622

623

624

625

626

627

628

629

630

631

632

633

634

635

636

637

638

639

640

641

642

643

644

645

646

647

648

649

650

651

652

653

654

655

656

657

658

659

660

661

662

663

664

665

666

667

668

669

670

671

672

673

674

675

676

677

678

679

680

681

682

683

684

685

686

687

688

689

690

691

692

693

694

695

696

697

698

699

700

701

702

703

704

705

706

707

708

709

710

711

712

713

714

715

716

717

718

719

720

721

722

723

724

725

726

727

728

729

730

731

732

733

734

735

736

737

738

739

740

741

742

743

744

745

267A

269A

271A

273A

273B

273C

491A

375A

389A

389B

746

747

748

749

750

751

752

753

754

755

756

757

758

759

760

761

762

763

764

765

766

767

768

769

770

771

772

773

774

775

776

777

778

779

780

781

639A

II. Methods

Another aspect of the disclosure provides methods of treating patientssuffering from a viral infection, e.g., a coronaviral infection. Inparticular, in certain embodiments, the disclosure provides a method oftreating the below medical indications comprising administering to asubject in need thereof a therapeutically effective amount of a compounddescribed herein, such as a compound of Formula II, II-A, II-B, II-C,II-D-I, II-D-II, II-E, and II-I.

In certain embodiments, the disclosure provides a method of amelioratingor treating a viral infection in a patient in need thereof, comprisingadministering to the patient a therapeutically effective amount of anyof the compounds described herein. In some embodiments, the viralinfection is from a virus selected from the group consisting of an RNAvirus, a DNA virus, a coronavirus, a papillomavirus, a pneumovirus, apicornavirus, an influenza virus, an adenovirus, a cytomegalovirus, apolyomavirus, a poxvirus, a flavivirus, an alphavirus, an ebola virus, amorbillivirus, an enterovirus, an orthopneumovirus, a lentivirus,arenavirus, a herpes virus, and a hepatovirus. In certain embodiments,the viral infection is a coronavirus infection. In some embodiments, theviral infection is a coronavirus selected from the group consisting of:229E alpha coronavirus, NL63 alpha coronavirus, OC43 beta coronavirus,HKU1 beta coronavirus, Middle East Respiratory Syndrome (MERS)coronavirus (MERS-CoV), severe acute respiratory syndrome (SARS)coronavirus (SARS-CoV), and SARS-CoV-2 (COVID-19). In embodiments, theviral infection is SARS-CoV-2.

In some embodiments, the viral infection is from a virus selected fromthe group consisting of calicivimses, MD145, murine norovirus, vesicularexanthema of swine virus, abbit hemorrhagic disease virus, porcineteschovirus, bovine coronavirus, feline infectious peritonitis virus,EV-68 virus, EV-71 virus, poliovirus, norovirus, human rhinovirus (HRV),hepatitis A virus (HAV) and foot-and-mouth disease virus (FMDV).

In embodiments, the viral infection is an arenavirus infection. In someembodiments, the arenavirus is selected from the group consisting of:Junin virus, Lassa virus, Lujo virus, Machupo virus, and Sabia virus. Insome embodiments, the viral infection is an influenza infection. In someembodiments, the influenza is influenza H1N1, H3N2 or H5N1.

Another aspect of the disclosure provides methods of treating patientssuffering from a viral infection, e.g., a noroviral infection. In someembodiments, the disclosure provides a method of treating a viralinfection from a norovirus in a patient in need thereof, comprisingadministering to the patient a therapeutically effective amount of anyof the compounds described herein.

Also provided herein, in certain embodiments, is a method of inhibitingtransmission of a virus, a method of inhibiting viral replication, amethod of minimizing expression of viral proteins, or a method ofinhibiting virus release, comprising administering a therapeuticallyeffective amount of a compound described herein to a patient sufferingfrom the virus, and/or contacting an effective amount of a compounddescribed herein with a virally infected cell. In some embodiments, themethod further comprises administering another therapeutic. In someembodiments, the method further comprises administering an additionalanti-viral therapeutic. In embodiments, the anti-viral therapeutic isselected from the group consisting of ribavirin, favipiravir, ST-193,oseltamivir, zanamivir, peramivir, danoprevir, ritonavir, remdesivir,cobicistat, elvitegravir, emtricitabine, tenofovir, tenofovirdisoproxil, tenofovir alafenamide hemifumarate, abacavir, dolutegravir,efavirenz, elbasvir, ledipasvir, glecaprevir, sofosbuvir, bictegravir,dasabuvir, lamivudine, atazanavir, ombitasvir, lamivudine, stavudine,nevirapine, rilpivirine, paritaprevir, simeprevir, daclatasvir,grazoprevir, pibrentasvir, adefovir, amprenavir, ampligen, aplaviroc,anti-caprine antibody, balavir, cabotegravir, cytarabine, ecoliever,epigallocatechin gallate, etravirine, fostemsavir, gemcitabine,griffithsin, imunovir, indinavir, maraviroc, methisazone, MK-2048,nelfmavir, nevirapine, nitazoxanide, norvir, plerixafor, PRO 140,raltegravir, pyramidine, saquinavir, telbivudine, TNX-355, valacyclovir,VIR-576, and zalcitabine. In some embodiments, the another therapeuticis selected from the group consisting of protease inhibitors, fusioninhibitors, M2 proton channel blockers, polymerase inhibitors,6-endonuclease inhibitors, neuraminidase inhibitors, reversetranscriptase inhibitor, aciclovir, acyclovir, protease inhibitors,arbidol, atazanavir, atripla, boceprevir, cidofovir, combivir,darunavir, docosanol, edoxudine, entry inhibitors, entecavir,famciclovir, fomivirsen, fosamprenavir, foscarnet, fosfonet,ganciclovir, ibacitabine, immunovir, idoxuridine, imiquimod, inosine,integrase inhibitor, interferons, lopinavir, loviride, moroxydine,nexavir, nucleoside analogues, penciclovir, pleconaril, podophyllotoxin,ribavirin, tipranavir, trifluridine, trizivir, tromantadine, truvada,valaciclovir, valganciclovir, vicriviroc, vidarabine, viramidine, andzodovudine. In embodiments, the additional anti-viral therapeutic isselected from the group consisting of lamivudine, an interferon alpha, aVAP anti-idiotypic antibody, enfuvirtide, amantadine, rimantadine,pleconaril, aciclovir, zidovudine, fomivirsen, a morpholino, a proteaseinhibitor, double-stranded RNA activated caspase oligomerizer (DRACO),rifampicin, zanamivir, oseltamivir, danoprevir, ritonavir, remdesivir,cobicistat, elvitegravir, emtricitabine, tenofovir, tenofovirdisoproxil, tenofovir alafenamide hemifumarate, abacavir, dolutegravir,efavirenz, elbasvir, ledipasvir, glecaprevir, sofosbuvir, bictegravir,dasabuvir, lamivudine, atazanavir, ombitasvir, lamivudine, stavudine,nevirapine, rilpivirine, paritaprevir, simeprevir, daclatasvir,grazoprevir, pibrentasvir, adefovir, amprenavir, ampligen, aplaviroc,anti-caprine antibody, balavir, cabotegravir, cytarabine, ecoliever,epigallocatechin gallate, etravirine, fostemsavir, gemcitabine,griffithsin, imunovir, indinavir, maraviroc, methisazone, MK-2048,nelfmavir, nevirapine, nitazoxanide, norvir, plerixafor, PRO 140,raltegravir, pyramidine, saquinavir, telbivudine, TNX-355, valacyclovir,VIR-576, and zalcitabine.

Contemplated patients include not only humans, but other animals such ascompanion animals (e.g. dogs, cats), domestic animals (e.g. cow, swine),and wild animals (e.g. monkeys, bats, snakes).

Accordingly, in one embodiment, described herein is a method ofameliorating or treating a viral infection in a patient in need thereof,comprising administering to the patient a therapeutically effectiveamount of a compound described herein (e.g., a compound of Formula II,II-A, II-B, II-C, II-D-I, II-D-II, II-E, or II-I, as described herein)or a pharmaceutically acceptable salt thereof.

Other contemplated methods of treatment include method of treating orameliorating a virus infection condition or co-morbidity, byadministering a compound disclosed herein to a subject.

Exemplary co-morbidities include lung diseases, cardiac disorders,endocrine disorders, respiratory disorders, hepatic disorders, skeletaldisorders, psychiatric disorders, metabolic disorders, and reproductivedisorders.

In some embodiments, the viral infection is from a virus selected fromthe group consisting of an RNA virus, a DNA virus, a coronavirus, apapillomavirus, a pneumovirus, a picomavirus, an influenza virus, anadenovirus, a cytomegalovirus, a polyomavirus, a poxvirus, a flavivirus,an alphavirus, an ebola virus, a morbillivirus, an enterovirus, anorthopneumovirus, a lentivirus, arenavirus, a herpes virus, and ahepatovirus. In some embodiments, the viral infection is a coronavirusinfection. In some embodiments, the viral infection is a coronavirusselected from the group consisting of: 229E alpha coronavirus, NL63alpha coronavirus, OC43 beta coronavirus, HKU1 beta coronavirus, MiddleEast Respiratory Syndrome (MERS) coronavirus (MERS-CoV), severe acuterespiratory syndrome (SARS) coronavirus (SARS-CoV), and SARS-CoV-2(COVID-19). In some embodiments, the viral infection is SARS-CoV-2. Insome embodiments, the viral infection is an arenavirus infection. Insome embodiments, the arenavirus is selected from the group consistingof: Junin virus, Lassa virus, Lujo virus, Machupo virus, and Sabiavirus. In some embodiments, the viral infection is an influenzainfection. In some embodiments, the influenza is influenza H1N1, H3N2 orH5N1. In some embodiments, the viral infection is a respiratory viralinfection. In some embodiments, the viral infection is an upperrespiratory viral infection or a lower respiratory viral infection. Insome embodiments, the method further comprises administering anothertherapeutic.

In certain embodiments, the virus is selected from the group consistingof a retrovirus (e.g., human immunodeficiency virus (HIV), simianimmunodeficiency virus (SIV), human T-cell lymphotropic virus (HTLV)-1,HTLV-2, HTLV-3, HTLV-4), Ebola virus, hepatitis A virus, hepatitis Bvirus, hepatitis C virus, a herpes simplex virus (HSV) (e.g., HSV-1,HSV-2, varicella zoster virus, cytomegalovirus), an adenovirus, anorthomyxovirus (e.g., influenza virus A, influenza virus B, influenzavirus C, influenza virus D, togavirus), a flavivirus (e.g., denguevirus, Zika virus), West Nile virus, Rift Valley fever virus, anarenavirus, Crimean-Congo hemorrhagic fever virus, an echovirus, arhinovirus, coxsackie virus, a coronavirus (e.g., Severe acuterespiratory syndrome coronavirus 2 (SARS-CoV-2), coronavirus disease2019 (COVID-19), a respiratory syncytial virus, a mumps virus, arotavirus, measles virus, rubella virus, a parvovirus (e.g., anadeno-associated virus), a vaccinia virus, a variola virus, a molluscumvirus, bovine leukemia virus, bovine diarrhea virus, a poliovirus, St.Louis encephalitis virus, Japanese encephalitis virus, a tick-borneencephalitis virus, Murray Valley virus, Powassan virus, Rocio virus,louping-ill virus, Banzi virus, Iheus virus, Kokobera virus, Kunjinvirus, Alfuy virus, a rabies virus, a polyomavirus (e.g., JC virus, BKvirus), an alphavirus, and a rubivirus (e.g., rubella virus).

In certain embodiments, the disease or disorder is a viral infection,e.g., a disease or disorder selected from the group consisting ofacquired immune deficiency syndrome (AIDS), HTLV-1 associatedmyelopathy/tropical spastic paraparesis, Ebola virus disease, hepatitisA, hepatitis B, hepatitis C, herpes, herpes zoster, acute varicella,mononucleosis, respiratory infections, pneumonia, influenza, denguefever, encephalitis (e.g., Japanese encephalitis, St. Louisencephalitis, or tick-borne encephalitis such as Powassan encephalitis),West Nile fever, Rift Valley fever, Crimean-Congo hemorrhagic fever,Kyasanur Forest disease, Yellow fever, Zika fever, aseptic meningitis,myocarditis, common cold, lung infections, molloscum contagiosum,enzootic bovine leucosis, coronavirus disease 2019 (COVID-19), mumps,gastroenteritis, measles, rubella, slapped-cheek disease, smallpox,warts (e.g., genital warts), molluscum contagiosum, polio, rabies, andpityriasis rosea.

In some embodiments, the virus is an RNA virus (having a genome that iscomposed of RNA). RNA viruses may be single-stranded RNA (ssRNA) ordouble-stranded RNA (dsRNA). RNA viruses have high mutation ratescompared to DNA viruses, as RNA polymerase lacks proofreading capability(see Steinhauer D A, Holland J J (1987). “Rapid evolution of RNAviruses”. Annu. Rev. Microbiol. 41: 409-33). In some embodiments, theRNA virus is a positive-strand RNA virus (e.g., a SARS-CoV virus, poliovirus, Coxsackie virus, Enterovirus, Human rhinovirus, Foot/Mouthdisease virus, encephalomyocarditis virus, Dengue virus, Zika virus,Hepatitis C virus, or New Castle Disease virus).

RNA viruses are classified by the type of genome (double-stranded,negative (−), or positive (+) single-stranded). Double-stranded RNAviruses contain a number of different RNA molecules, each coding for oneor more viral proteins. Positive-sense ssRNA viruses utilize theirgenome directly as mRNA; ribosomes within the host cell translate mRNAinto a single protein that is then modified to form the various proteinsneeded for viral replication. One such protein is RNA-dependent RNApolymerase (RNA replicase), which copies the viral RNA in order to forma double-stranded, replicative form. Negative-sense ssRNA viruses havetheir genome copied by an RNA replicase enzyme to produce positive-senseRNA for replication. Therefore, the virus comprises an RNA replicaseenzyme. The resultant positive-sense RNA then acts as viral mRNA and istranslated by the host ribosomes. In some embodiments, the virus is adsRNA virus. In some embodiments, the virus is a negative ssRNA virus.In some embodiments, the virus is a positive ssRNA virus. In someembodiments, the positive ssRNA virus is a coronavirus.

SARS-CoV2, also sometimes referred to as the novel coronavirus of 2019or 2019-nCoV, is a positive-sense single-stranded RNA virus. SARS-CoV-2has four structural proteins, known as the S (spike), E (envelope), M(membrane), and N (nucleocapsid) proteins. The N protein holds the RNAgenome together; the S, E, and M proteins form the viral envelope. Spikeallows the virus to attach to the membrane of a host cell, such as theACE2 receptor in human cells (Kruse R. L. (2020), Therapeutic strategiesin an outbreak scenario to treat the novel coronavirus originating inWuhan, China (version 2). F1000Research, 9:72). SARS-CoV2 is the highlycontagious, causative viral agent of coronavirus disease 2019 (COVID19),a global pandemic.

In some embodiments, the virus is a DNA virus (having a genome that iscomposed of DNA). Exemplary DNA viruses include, without limitation,parvoviruses (e.g., adeno-associated viruses), adenoviruses,asfarviruses, herpesviruses (e.g., herpes simplex virus 1 and 2 (HSV-1and HSV-2), Epstein-Barr virus (EBV), cytomegalovirus (CMV)),papillomaviruses (e.g., HPV), polyomaviruses (e.g., simian vacuolatingvirus 40 (SV40)), and poxviruses (e.g., vaccinia virus, cowpox virus,smallpox virus, fowlpox virus, sheeppox virus, myxoma virus). ExemplaryRNA viruses include, without limitation, bunyaviruses (e.g.,hantavirus), coronaviruses, flaviviruses (e.g., yellow fever virus, westNile virus, dengue virus), hepatitis viruses (e.g., hepatitis A virus,hepatitis C virus, hepatitis E virus), influenza viruses (e.g.,influenza virus type A, influenza virus type B, influenza virus type C),measles virus, mumps virus, calicivirus, noroviruses (e.g., Norwalkvirus), poliovirus, respiratory syncytial virus (RSV), retroviruses(e.g., human immunodeficiency virus-1 (HIV-1)) and toroviruses.

The methods described herein may inhibit viral replication transmission,replication, assembly, or release, or minimize expression of viralproteins. In one embodiment, described herein is a method of inhibitingtransmission of a virus, a method of inhibiting viral replication, amethod of minimizing expression of viral proteins, or a method ofinhibiting virus release, comprising administering a therapeuticallyeffective amount of a compound described herein, or a pharmaceuticallyacceptable salt thereof, to a patient suffering from the virus, and/orcontacting an effective amount of a compound described herein or apharmaceutically acceptable salt thereof, with a virally infected cell.

Also described herein is a method of treating a respiratory disorder ina subject in need thereof, comprising administering to the patient atherapeutically effective amount of a compound described herein (e.g., acompound of Formula II, II-A, II-B, II-C, II-D-I, II-D-II, II-E, orII-I, etc. described herein) or a pharmaceutically acceptable saltthereof. In embodiments, the respiratory disorder is selected from thegroup consisting of chronic obstructive pulmonary disease (COPD),asthma, fibrosis, chronic asthma, acute asthma, lung disease secondaryto environmental exposures, acute lung infection, chronic lunginfection, al antitrypsin disease, cystic fibrosis and an autoimmunedisease.

Compounds described herein, e.g., a compound of Formula II, II-A, II-B,II-C, II-D-I, II-D-II, II-E, or II-I, etc. as defined herein, can beadministered in combination with one or more additional therapeuticagents to treat a disorder described herein, such as an infection by apathogen described herein, e.g., a virus, fungus, or protozoan. Forclarity, contemplated herein are both a fixed composition comprising adisclosed compound and another therapeutic agent such as disclosedherein, and methods of administering, separately a disclosed compoundand a disclosed therapeutic. For example, provided in the presentdisclosure is a pharmaceutical composition comprising a compounddescribed herein, e.g., a compound of Formula II, II-A, II-B, II-C,II-D-I, II-D-II, II-E, or II-I as defined herein, one or more additionaltherapeutic agents, and a pharmaceutically acceptable excipient. In someembodiments, a compound of Formula II, II-A, II-B, II-C, II-D-I,II-D-II, II-E, or II-I as defined herein and one additional therapeuticagent is administered. In some embodiments, a disclosed compound asdefined herein and two additional therapeutic agents are administered.In some embodiments, a disclosed compound as defined herein and threeadditional therapeutic agents are administered. Combination therapy canbe achieved by administering two or more therapeutic agents, each ofwhich is formulated and administered separately. For example, a compoundof Formula II, II-A, II-B, II-C, II-D-I, II-D-II, II-E, or II-I, etc. asdefined herein and an additional therapeutic agent can be formulated andadministered separately. Combination therapy can also be achieved byadministering two or more therapeutic agents in a single formulation,for example a pharmaceutical composition comprising a compound ofFormula II, II-A, II-B, II-C, II-D-I, II-D-II, II-E, or II-I as onetherapeutic agent and one or more additional therapeutic agents such asan antibiotic, a viral protease inhibitor, or an anti-viral nucleosideanti-metabolite. For example, a compound of Formula II, II-A, II-B,II-C, II-D-I, II-D-II, II-E, or II-I as defined herein and an additionaltherapeutic agent can be administered in a single formulation. Othercombinations are also encompassed by combination therapy. While the twoor more agents in the combination therapy can be administeredsimultaneously, they need not be. For example, administration of a firstagent (or combination of agents) can precede administration of a secondagent (or combination of agents) by minutes, hours, days, or weeks.Thus, the two or more agents can be administered within minutes of eachother or within 1, 2, 3, 6, 9, 12, 15, 18, or 24 hours of each other orwithin 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 14 days of each other orwithin 2, 3, 4, 5, 6, 7, 8, 9, or weeks of each other. In some caseseven longer intervals are possible. While in many cases it is desirablethat the two or more agents used in a combination therapy be present inwithin the patient's body at the same time, this need not be so.

Combination therapy can also include two or more administrations of oneor more of the agents used in the combination using different sequencingof the component agents. For example, if agent X and agent Y are used ina combination, one could administer them sequentially in any combinationone or more times, e.g., in the order X-Y-X, X-X-Y, Y-X-Y, Y-Y-X,X-X-Y-Y, etc.

In some embodiments, the one or more additional therapeutic agents thatmay be administered in combination with a compound provided herein canbe an antibiotic, a viral protease inhibitor, an anti-viralanti-metabolite, a lysosomotropic agent, a M2 proton channel blocker, apolymerase inhibitor (e.g., EIDD-2801), a neuraminidase inhibitor, areverse transcriptase inhibitor, a viral entry inhibitor, an integraseinhibitor, interferons (e.g., types I, II, and III), or a nucleosideanalogue.

In some embodiments, methods described herein further compriseadministering an additional anti-viral therapeutic. In some embodiments,the anti-viral therapeutic is selected from the group consisting ofribavirin, favipiravir, ST-193, oseltamivir, zanamivir, peramivir,danoprevir, ritonavir, remdesivir, cobicistat, elvitegravir,emtricitabine, tenofovir, tenofovir disoproxil, tenofovir alafenamidehemifumarate, abacavir, dolutegravir, efavirenz, elbasvir, ledipasvir,glecaprevir, sofosbuvir, bictegravir, dasabuvir, lamivudine, atazanavir,ombitasvir, lamivudine, stavudine, nevirapine, rilpivirine,paritaprevir, simeprevir, daclatasvir, grazoprevir, pibrentasvir,adefovir, amprenavir, ampligen, aplaviroc, anti-caprine antibody,balavir, cabotegravir, cytarabine, ecoliever, epigallocatechin gallate,etravirine, fostemsavir, gemcitabine, griffithsin, imunovir, indinavir,maraviroc, methisazone, MK-2048, nelfmavir, nevirapine, nitazoxanide,norvir, plerixafor, PRO 140, raltegravir, pyramidine, saquinavir,telbivudine, TNX-355, valacyclovir, VIR-576, and zalcitabine. In someembodiments, the another therapeutic is selected from the groupconsisting of protease inhibitors (e.g., nafamostat, camostat, gabexate,epsilon-aminocapronic acid and aprotinin), fusion inhibitors (e.g.,BMY-27709, CL 61917, and CL 62554), M2 proton channel blockers (e.g.,amantadine and rimantadine), polymerase inhibitors (e.g.,2-deoxy-2′fluoroguanosides (2′-fluoroGuo), 6-endonuclease inhibitors(e.g., L-735,822 and flutamide) neuraminidase inhibitors (e.g.,zanamivir (Relenza), oseltamivir, peramivir and ABT-675 (A-315675),reverse transcriptase inhibitor (e.g., abacavir, adefovir, delavirdine,didanosine, efavirenz, emtricitabine, lamivudine, nevirapine, stavudine,tenofovir, tenofovir disoproxil, and zalcitabine), acyclovir, acyclovir,protease inhibitors (e.g., amprenavir, indinavir, nelfinavir, ritonavir,and saquinavir), arbidol, atazanavir, atripla, boceprevir, cidofovir,combivir, darunavir, docosanol, edoxudine, entry inhibitors (e.g.,enfuvirtide and maraviroc), entecavir, famciclovir, fomivirsen,fosamprenavir, foscarnet, fosfonet, ganciclovir, ibacitabine, immunovir,idoxuridine, imiquimod, inosine, integrase inhibitor (e.g.,raltegravir), interferons (e.g., types I, II, and III), lopinavir,loviride, moroxydine, nexavir, nucleoside analogues (e.g., aciclovir),penciclovir, pleconaril, podophyllotoxin, ribavirin, tipranavir,trifluridine, trizivir, tromantadine, truvada, valaciclovir,valganciclovir, vicriviroc, vidarabine, viramidine, and zodovudine. Insome embodiments, the additional anti-viral therapeutic is selected fromthe group consisting of lamivudine, an interferon alpha, a VAPanti-idiotypic antibody, enfuvirtide, amantadine, rimantadine,pleconaril, aciclovir, zidovudine, fomivirsen, a morpholino, a proteaseinhibitor, double-stranded RNA activated caspase oligomerizer (DRACO),rifampicin, zanamivir, oseltamivir, danoprevir, ritonavir, remdesivir,cobicistat, elvitegravir, emtricitabine, tenofovir, tenofovirdisoproxil, tenofovir alafenamide hemifumarate, abacavir, dolutegravir,efavirenz, elbasvir, ledipasvir, glecaprevir, sofosbuvir, bictegravir,dasabuvir, lamivudine, atazanavir, ombitasvir, lamivudine, stavudine,nevirapine, rilpivirine, paritaprevir, simeprevir, daclatasvir,grazoprevir, pibrentasvir, adefovir, amprenavir, ampligen, aplaviroc,anti-caprine antibody, balavir, cabotegravir, cytarabine, ecoliever,epigallocatechin gallate, etravirine, fostemsavir, gemcitabine,griffithsin, imunovir, indinavir, maraviroc, methisazone, MK-2048,nelfmavir, nevirapine, nitazoxanide, norvir, plerixafor, PRO 140,raltegravir, pyramidine, saquinavir, telbivudine, TNX-355, valacyclovir,VIR-576, and zalcitabine. In some embodiments, the another therapeuticis selected from the group consisting of quinine (optionally incombination with clindamycin), chloroquine, amodiaquine, artemisinin andits derivatives (e.g., artemether, artesunate, dihydroartemisinin,arteether), doxycycline, pyrimethamine, mefloquine, halofantrine,hydroxychloroquine, eflornithine, nitazoxanide, ornidazole, paromomycin,pentamidine, primaquine, pyrimethamine, proguanil (optionally incombination with atovaquone), a sulfonamide (e.g., sulfadoxine,sulfamethoxypyridazine), tafenoquine, tinidazole and a PPT1 inhibitor(including Lys05 and DC661). In some embodiments, the anothertherapeutic is an antibiotic. In some embodiments, the antibiotic is apenicillin antibiotic, a quinolone antibiotic, a tetracyclineantibiotic, a macrolide antibiotic, a lincosamide antibiotic, acephalosporin antibiotic, or an RNA synthetase inhibitor. In someembodiments, the antibiotic is selected from the group consisting ofazithromycin, vancomycin, metronidazole, gentamicin, colistin,fidaxomicin, telavancin, oritavancin, dalbavancin, daptomycin,cephalexin, cefuroxime, cefadroxil, cefazolin, cephalothin, cefaclor,cefamandole, cefoxitin, cefprozil, ceftobiprole, cipro, Levaquin,floxin, tequin, avelox, norflox, tetracycline, minocycline,oxytetracycline, doxycycline, amoxicillin, ampicillin, penicillin V,dicloxacillin, carbenicillin, methicillin, ertapenem, doripenem,imipenem/cilastatin, meropenem, amikacin, kanamycin, neomycin,netilmicin, tobramycin, paromomycin, cefixime, cefdinir, cefditoren,cefoperazone, cefotaxime, ceftazidime, ceftibuten, ceftizoxime,ceftriaxone, cefoxotin, and streptomycin. In some embodiments, theantibiotic is azithromycin.

In some embodiments, the one or more additional therapeutic agents thatmay be administered in combination with a compound provided herein canbe selected from the group consisting of ribavirin, favipiravir, ST-193,oseltamivir, zanamivir, peramivir, danoprevir, ritonavir, remdesivir,cobicistat, elvitegravir, emtricitabine, tenofovir, tenofovirdisoproxil, tenofovir alafenamide hemifumarate, abacavir, dolutegravir,efavirenz, elbasvir, ledipasvir, glecaprevir, sofosbuvir, bictegravir,dasabuvir, lamivudine, atazanavir, ombitasvir, lamivudine, stavudine,nevirapine, rilpivirine, paritaprevir, simeprevir, daclatasvir,grazoprevir, pibrentasvir, adefovir, amprenavir, ampligen, aplaviroc,anti-caprine antibody, balavir, cabotegravir, cytarabine, ecoliever,epigallocatechin gallate, etravirine, fostemsavir, gemcitabine,griffithsin, imunovir, indinavir, maraviroc, methisazone, MK-2048,nelfmavir, nevirapine, nitazoxanide, norvir, plerixafor, PRO 140,raltegravir, pyramidine, saquinavir, telbivudine, TNX-355, valacyclovir,VIR-576, and zalcitabine.

In some embodiments, the compounds described herein (e.g. a compound ofFormula II, II-A, II-B, II-C, II-D-I, II-D-II, II-E, or II-I, etc.) andpharmaceutically acceptable salts thereof may be used in combinationwith one or more other agents which may be useful in the prevention ortreatment of respiratory disease, inflammatory disease, autoimmunedisease, for example; anti-histamines, corticosteroids, (e.g.,fluticasone propionate, fluticasone furoate, beclomethasonedipropionate, budesonide, ciclesonide, mometasone furoate,triamcinolone, flunisolide), NSAIDs, leukotriene modulators (e.g.,montelukast, zafirlukast.pranlukast), tryptase inhibitors, IKK2inhibitors, p38 inhibitors, Syk inhibitors, protease inhibitors such aselastase inhibitors, integrin antagonists (e.g., beta-2 integrinantagonists), adenosine A2a agonists, mediator release inhibitors suchas sodium chromoglycate, 5-lipoxygenase inhibitors (zyflo), DP1antagonists, DP2 antagonists, PI3K delta inhibitors, ITK inhibitors, LP(lysophosphatidic) inhibitors or FLAP (5-lipoxygenase activatingprotein) inhibitors (e.g., sodium3-(3-(tert-butylthio)-1-(4-(6-ethoxypyridin-3-yl)benzyl)-5-((5-ethylpyridin-2-yl)methoxy)-1H-indol-2-yl)-2,2-dimethylpropanoate),bronchodilators (e.g., muscarinic antagonists, beta-2 agonists),methotrexate, and similar agents; monoclonal antibody therapy such asanti-IgE, anti-TNF, anti-IL-5, anti-IL-6, anti-IL-12, anti-IL-1 andsimilar agents; cytokine receptor therapies e.g. etanercept and similaragents; antigen non-specific immunotherapies (e.g. interferon or othercytokines/chemokines, chemokine receptor modulators such as CCR3, CCR4or CXCR2 antagonists, other cytokine/chemokine agonists or antagonists,TLR agonists and similar agents), suitable anti-infective agentsincluding antibiotic agents, antifungal agents, anthelmintic agents,antimalarial agents, antiprotozoal agents and antituberculosis agents.

In some embodiments, the additional therapeutic agents can be kinaseinhibitors including but not limited to erlotinib, gefitinib, neratinib,afatinib, osimertinib, lapatanib, crizotinib, brigatinib, ceritinib,alectinib, lorlatinib, everolimus, temsirolimus, abemaciclib, LEE011,palbociclib, cabozantinib, sunitinib, pazopanib, sorafenib, regorafenib,sunitinib, axitinib, dasatinib, imatinib, nilotinib, ponatinib,idelalisib, ibrutinib, Loxo 292, larotrectinib, and quizartinib.

In some embodiments, the additional therapeutic agents can betherapeutic anti-viral vaccines.

In some embodiments, the additional therapeutic agents can beimmunomodulatory agents including but not limited to anti-PD-1 oranti-PDL-1 therapeutics including pembrolizumab, nivolumab,atezolizumab, durvalumab, BMS-936559, or avelumab, anti-TIM3(anti-HAVcr2) therapeutics including but not limited to TSR-022 orMBG453, anti-LAG3 therapeutics including but not limited to relatlimab,LAG525, or TSR-033, anti-4-1BB (anti-CD37, anti-TNFRSF9), CD40 agonisttherapeutics including but not limited to SGN-40, CP-870,893 orRO7009789, anti-CD47 therapeutics including but not limited to Hu5F9-G4,anti-CD20 therapeutics, anti-CD38 therapeutics, STING agonists includingbut not limited to ADU-S100, MK-1454, ASA404, or amidobenzimidazoles,anthracyclines including but not limited to doxorubicin ormitoxanthrone, hypomethylating agents including but not limited toazacytidine or decitabine, other immunomodulatory therapeutics includingbut not limited to epidermal growth factor inhibitors, statins,metformin, angiotensin receptor blockers, thalidomide, lenalidomide,pomalidomide, prednisone, or dexamethasone. In some embodiments, theadditional therapeutic agent is a p2-adrenoreceptor agonist including,but not limited to, vilanterol, salmeterol, salbutamol.formoterol,salmefamol, fenoterol carmoterol, etanterol, naminterol, clenbuterol,pirbuterol.flerbuterol, reproterol, bambuterol, indacaterol, terbutalineand salts thereof, for example the xinafoate(1-hydroxy-2-naphthalenecarboxylate) salt of salmeterol, the sulphatesalt of salbutamol or the fumarate salt of formoterol. In someembodiments, the additional therapeutic agent is an anticholinergicagent, including, but not limited to, umeclidinium (for example, as thebromide), ipratropium (for example, as the bromide), oxitropium (forexample, as the bromide) and tiotropium (for example, as the bromide).

In particular, in certain embodiments, the disclosure provides a methodof treating the above medical indications comprising administering asubject in need thereof a therapeutically effective amount of a compounddescribed herein, such as a disclosed compound.

The term “boosting amount” or “boosting dose” is the amount of acompound needed to improve the pharmacokinetics of a second compound (orincrease availability or exposure). The boosting amount or boosting dosemay improve the pharmacokinetics (or increase availability or exposure)of the second compound to a level to therapeutic levels in a subject.

In one embodiment, the disclosure provides for a disclosed compound tobe administered together with an antiviral therapeutic such as disclosedherein, and e.g., thereby boosting the dose of the anti-viraltherapeutic or therapeutics. Such a boost combination may be used, e.g.,as prophylactic or therapeutic treatment of a viral infection in asubject in need thereof. In one embodiment, the protease inhibitor is acompound described herein (e.g. a compound of Formula II, II-A, II-B,II-C, II-D-I, II-D-II, II-E, or II-I, etc.).

III. Reversible or Irreversible Conjugates

In certain embodiments, provided herein are conjugates represented byFormula III:

wherein Cys₁₄₅ is cysteine at position 145 or equivalent active sitecysteine on a CL or 3CL protease; IR is a viral protease inhibitor; andwherein the compound that forms the conjugate comprises a —CN warhead.

IV. Pharmaceutical Compositions and Kits

Another aspect of the disclosure provides pharmaceutical compositionscomprising compounds as disclosed herein formulated together with apharmaceutically acceptable carrier. In particular, the presentdisclosure provides pharmaceutical compositions comprising compounds asdisclosed herein formulated together with one or more pharmaceuticallyacceptable carriers. These formulations include those suitable for oral,rectal, topical, buccal, parenteral (e.g., subcutaneous, intramuscular,intradermal, or intravenous) rectal, vaginal, or aerosol administration,although the most suitable form of administration in any given case willdepend on the degree and severity of the condition being treated and onthe nature of the particular compound being used. For example, disclosedcompositions may be formulated as a unit dose, and/or may be formulatedfor oral or subcutaneous administration.

Exemplary pharmaceutical compositions of this disclosure may be used inthe form of a pharmaceutical preparation, for example, in solid,semisolid or liquid form, which contains one or more of the compound ofthe disclosure, as an active ingredient, in admixture with an organic orinorganic carrier or excipient suitable for external, enteral orparenteral applications. The active ingredient may be compounded, forexample, with the usual non-toxic, pharmaceutically acceptable carriersfor tablets, pellets, capsules, suppositories, solutions, emulsions,suspensions, and any other form suitable for use. The active objectcompound is included in the pharmaceutical composition in an amountsufficient to produce the desired effect upon the process or conditionof the disease.

For preparing solid compositions such as tablets, the principal activeingredient may be mixed with a pharmaceutical carrier, e.g.,conventional tableting ingredients such as corn starch, lactose,sucrose, sorbitol, talc, stearic acid, magnesium stearate, dicalciumphosphate or gums, and other pharmaceutical diluents, e.g., water, toform a solid preformulation composition containing a homogeneous mixtureof a compound of the disclosure, or a non-toxic pharmaceuticallyacceptable salt thereof. When referring to these preformulationcompositions as homogeneous, it is meant that the active ingredient isdispersed evenly throughout the composition so that the composition maybe readily subdivided into equally effective unit dosage forms such astablets, pills and capsules.

In solid dosage forms for oral administration (capsules, tablets, pills,dragees, powders, granules and the like), the subject composition ismixed with one or more pharmaceutically acceptable carriers, such assodium citrate or dicalcium phosphate, and/or any of the following: (1)fillers or extenders, such as starches, lactose, sucrose, glucose,mannitol, and/or silicic acid; (2) binders, such as, for example,carboxymethylcellulose, alginates, gelatin, polyvinyl pyrrolidone,sucrose and/or acacia; (3) humectants, such as glycerol; (4)disintegrating agents, such as agar-agar, calcium carbonate, potato ortapioca starch, alginic acid, certain silicates, and sodium carbonate;(5) solution retarding agents, such as paraffin; (6) absorptionaccelerators, such as quaternary ammonium compounds; (7) wetting agents,such as, for example, acetyl alcohol and glycerol monostearate; (8)absorbents, such as kaolin and bentonite clay; (9) lubricants, such atalc, calcium stearate, magnesium stearate, solid polyethylene glycols,sodium lauryl sulfate, and mixtures thereof; and (10) coloring agents.In the case of capsules, tablets and pills, the compositions may alsocomprise buffering agents. Solid compositions of a similar type may alsobe employed as fillers in soft and hard-filled gelatin capsules usingsuch excipients as lactose or milk sugars, as well as high molecularweight polyethylene glycols and the like.

A tablet may be made by compression or molding, optionally with one ormore accessory ingredients. Compressed tablets may be prepared usingbinder (for example, gelatin or hydroxypropylmethyl cellulose),lubricant, inert diluent, preservative, disintegrant (for example,sodium starch glycolate or cross-linked sodium carboxymethyl cellulose),surface-active or dispersing agent. Molded tablets may be made bymolding in a suitable machine a mixture of the subject compositionmoistened with an inert liquid diluent. Tablets, and other solid dosageforms, such as dragees, capsules, pills and granules, may optionally bescored or prepared with coatings and shells, such as enteric coatingsand other coatings well-known in the pharmaceutical-formulating art.

Compositions for inhalation or insufflation include solutions andsuspensions in pharmaceutically acceptable, aqueous or organic solvents,or mixtures thereof, and powders. Liquid dosage forms for oraladministration include pharmaceutically acceptable emulsions,microemulsions, solutions, suspensions, syrups and elixirs. In additionto the subject composition, the liquid dosage forms may contain inertdiluents commonly used in the art, such as, for example, water or othersolvents, solubilizing agents and emulsifiers, such as ethyl alcohol,isopropyl alcohol, ethyl carbonate, ethyl acetate, benzyl alcohol,benzyl benzoate, propylene glycol, 1,3-butylene glycol, oils (inparticular, cottonseed, groundnut, corn, germ, olive, castor and sesameoils), glycerol, tetrahydrofuryl alcohol, polyethylene glycols and fattyacid esters of sorbitan, cyclodextrins and mixtures thereof.

Suspensions, in addition to the subject composition, may containsuspending agents as, for example, ethoxylated isostearyl alcohols,polyoxyethylene sorbitol and sorbitan esters, microcrystallinecellulose, aluminum metahydroxide, bentonite, agar-agar and tragacanth,and mixtures thereof.

Formulations for rectal or vaginal administration may be presented as asuppository, which may be prepared by mixing a subject composition withone or more suitable non-irritating excipients or carriers comprising,for example, cocoa butter, polyethylene glycol, a suppository wax or asalicylate, and which is solid at room temperature, but liquid at bodytemperature and, therefore, will melt in the body cavity and release theactive agent.

Dosage forms for transdermal administration of a subject compositioninclude powders, sprays, ointments, pastes, creams, lotions, gels,solutions, patches and inhalants. The active component may be mixedunder sterile conditions with a pharmaceutically acceptable carrier, andwith any preservatives, buffers, or propellants which may be required.

The ointments, pastes, creams and gels may contain, in addition to asubject composition, excipients, such as animal and vegetable fats,oils, waxes, paraffins, starch, tragacanth, cellulose derivatives,polyethylene glycols, silicones, bentonites, silicic acid, talc and zincoxide, or mixtures thereof.

Powders and sprays may contain, in addition to a subject composition,excipients such as lactose, talc, silicic acid, aluminum hydroxide,calcium silicates and polyamide powder, or mixtures of these substances.Sprays may additionally contain customary propellants, such aschlorofluorohydrocarbons and volatile unsubstituted hydrocarbons, suchas butane and propane.

Compositions and compounds of the present disclosure may alternativelybe administered by aerosol. This is accomplished by preparing an aqueousaerosol, liposomal preparation or solid particles containing thecompound. A non-aqueous (e.g., fluorocarbon propellant) suspension couldbe used. Sonic nebulizers may be used because they minimize exposing theagent to shear, which may result in degradation of the compoundscontained in the subject compositions. Ordinarily, an aqueous aerosol ismade by formulating an aqueous solution or suspension of a subjectcomposition together with conventional pharmaceutically acceptablecarriers and stabilizers. The carriers and stabilizers vary with therequirements of the particular subject composition, but typicallyinclude non-ionic surfactants (Tweens, Pluronics, or polyethyleneglycol), innocuous proteins like serum albumin, sorbitan esters, oleicacid, lecithin, amino acids such as glycine, buffers, salts, sugars orsugar alcohols. Aerosols generally are prepared from isotonic solutions.

Pharmaceutical compositions of this disclosure suitable for parenteraladministration comprise a subject composition in combination with one ormore pharmaceutically-acceptable sterile isotonic aqueous or non-aqueoussolutions, dispersions, suspensions or emulsions, or sterile powderswhich may be reconstituted into sterile injectable solutions ordispersions just prior to use, which may contain antioxidants, buffers,bacteriostats, solutes which render the formulation isotonic with theblood of the intended recipient or suspending or thickening agents.

Examples of suitable aqueous and non-aqueous carriers which may beemployed in the pharmaceutical compositions of the disclosure includewater, ethanol, polyols (such as glycerol, propylene glycol,polyethylene glycol, and the like), and suitable mixtures thereof,vegetable oils, such as olive oil, and injectable organic esters, suchas ethyl oleate and cyclodextrins. Proper fluidity may be maintained,for example, by the use of coating materials, such as lecithin, by themaintenance of the required particle size in the case of dispersions,and by the use of surfactants

In another aspect, the disclosure provides enteral pharmaceuticalformulations including a disclosed compound and an enteric material; anda pharmaceutically acceptable carrier or excipient thereof. Entericmaterials refer to polymers that are substantially insoluble in theacidic environment of the stomach, and that are predominantly soluble inintestinal fluids at specific pHs. The small intestine is the part ofthe gastrointestinal tract (gut) between the stomach and the largeintestine, and includes the duodenum, jejunum, and ileum. The pH of theduodenum is about 5.5, the pH of the jejunum is about 6.5 and the pH ofthe distal ileum is about 7.5. Accordingly, enteric materials are notsoluble, for example, until a pH of about 5.0, of about 5.2, of about5.4, of about 5.6, of about 5.8, of about 6.0, of about 6.2, of about6.4, of about 6.6, of about 6.8, of about 7.0, of about 7.2, of about7.4, of about 7.6, of about 7.8, of about 8.0, of about 8.2, of about8.4, of about 8.6, of about 8.8, of about 9.0, of about 9.2, of about9.4, of about 9.6, of about 9.8, or of about 10.0. Exemplary entericmaterials include cellulose acetate phthalate (CAP), hydroxypropylmethylcellulose phthalate (HPMCP), polyvinyl acetate phthalate (PVAP),hydroxypropyl methylcellulose acetate succinate (HPMCAS), celluloseacetate trimellitate, hydroxypropyl methylcellulose succinate, celluloseacetate succinate, cellulose acetate hexahydrophthalate, cellulosepropionate phthalate, cellulose acetate maleate, cellulose acetatebutyrate, cellulose acetate propionate, copolymer of methylmethacrylicacid and methyl methacrylate, copolymer of methyl acrylate,methylmethacrylate and methacrylic acid, copolymer of methylvinyl etherand maleic anhydride (Gantrez ES series), ethylmethyacrylate-methylmethacrylate-chlorotrimethylammonium ethyl acrylatecopolymer, natural resins such as zein, shellac and copal collophorium,and several commercially available enteric dispersion systems (e. g.,Eudragit L30D55, Eudragit FS30D, Eudragit L100, Eudragit S100, KollicoatEMM30D, Estacryl 30D, Coateric, and Aquateric). The solubility of eachof the above materials is either known or is readily determinable invitro. The foregoing is a list of possible materials, but one of skillin the art with the benefit of the disclosure would recognize that it isnot comprehensive and that there are other enteric materials that wouldmeet the objectives of the present disclosure.

Advantageously, the disclosure also provides kits for use by a e.g. aconsumer in need of 3CL inhibitor. Such kits include a suitable dosageform such as those described above and instructions describing themethod of using such dosage form to mediate, reduce or preventinflammation. The instructions would direct the consumer or medicalpersonnel to administer the dosage form according to administrationmodes known to those skilled in the art. Such kits could advantageouslybe packaged and sold in single or multiple kit units. An example of sucha kit is a so-called blister pack. Blister packs are well-known in thepackaging industry and are being widely used for the packaging ofpharmaceutical unit dosage forms (tablets, capsules, and the like).Blister packs generally consist of a sheet of relatively stiff materialcovered with a foil of a preferably transparent plastic material. Duringthe packaging process recesses are formed in the plastic foil. Therecesses have the size and shape of the tablets or capsules to bepacked. Next, the tablets or capsules are placed in the recesses and thesheet of relatively stiff material is sealed against the plastic foil atthe face of the foil which is opposite from the direction in which therecesses were formed. As a result, the tablets or capsules are sealed inthe recesses between the plastic foil and the sheet. Preferably thestrength of the sheet is such that the tablets or capsules can beremoved from the blister pack by manually applying pressure on therecesses whereby an opening is formed in the sheet at the place of therecess. The tablet or capsule can then be removed via said opening.

It may be desirable to provide a memory aid on the kit, e.g., in theform of numbers next to the tablets or capsules whereby the numberscorrespond with the days of the regimen which the tablets or capsules sospecified should be ingested. Another example of such a memory aid is acalendar printed on the card, e.g., as follows “First Week, Monday,Tuesday, . . . etc. . . . Second Week, Monday, Tuesday, . . . ” etc.Other variations of memory aids will be readily apparent. A “daily dose”can be a single tablet or capsule or several pills or capsules to betaken on a given day. Also, a daily dose of a first compound can consistof one tablet or capsule while a daily dose of the second compound canconsist of several tablets or capsules and vice versa. The memory aidshould reflect this.

Also contemplated herein are methods and compositions that include asecond active agent or administering a second active agent. For example,in addition to having a viral infection, a subject or patient canfurther have viral infection- or virus-related co-morbidities, i.e.,diseases and other adverse health conditions associated with,exacerbated by, or precipitated by being infected by a virus.Contemplated herein are disclosed compounds in combination with at leastone other agent that has previously been shown to treat thesevirus-related conditions.

EXAMPLES

The compounds described herein can be prepared in a number of ways basedon the teachings contained herein and synthetic procedures known in theart. In the description of the synthetic methods described below, it isto be understood that all proposed reaction conditions, including choiceof solvent, reaction atmosphere, reaction temperature, duration of theexperiment and workup procedures, can be chosen to be the conditionsstandard for that reaction, unless otherwise indicated. It is understoodby one skilled in the art of organic synthesis that the functionalitypresent on various portions of the molecule should be compatible withthe reagents and reactions proposed. Substituents not compatible withthe reaction conditions will be apparent to one skilled in the art, andalternate methods are therefore indicated. The starting materials forthe examples are either commercially available or are readily preparedby standard methods from known materials.

At least some of the compounds identified as “Intermediates” herein arecontemplated as compounds of the disclosure.

¹H NMR spectra are recorded at ambient temperature using e.g., a VarianUnity Inova (400 MHz) spectrometer with a triple resonance 5 mm probefor Example compounds, and either a Bruker Avance DRx (400 MHz)spectrometer or a Bruker Avance DPX (300 MHz) spectrometer forIntermediate compounds. Chemical shifts are expressed in ppm relative totetramethylsilane. The following abbreviations have been used: br=broadsignal, s=singlet, d=doublet, dd=double doublet, dt=double triplet,ddd=double doublet, t=triplet, td=triple doublet, tdd=triple doubledoublet, q=quartet, m=multiplet.

Mass Spectrometry (LCMS) experiments to determine retention times andassociated mass ions were performed using the following methods.

ABBREVIATIONS

-   AcOH Acetic acid-   Boc tert-Butoxycarbonyl protecting group-   DCM Dichloromethane-   DIEA N,N-Diisopropylethylamine-   DIPEA N,N-Diisopropylethylamine-   DMAP 4-Dimethylaminopyridine-   DMF Dimethylformamide-   EA Ethyl Acetate-   EtOAc Ethyl Acetate-   EDCI 1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide-   EtOH Ethanol-   HATU    (1-[Bis(dimethylamino)methylene]-1H-1,2,3-triazolo[4,5-b]pyridinium    3-oxide hexafluorophosphate-   HOBt Hydroxybenzotirazole-   LiHMDS Lithium bis(trimethylsilyl)amide-   MeOH Methanol-   PE Petroleum Ether-   PMA Phosphomolybdic acid-   Pht Phthaloyl-   T₃P Propanephosphonic acid anhydride-   TEA Triethylamine-   TFA Trifluoroacetic acid-   TFAA Trifluoroacetic anhydride-   THF Tetrahydrofuran

General Chemistry

Exemplary compounds described herein are available by the generalsynthetic method illustrated in the Scheme below, including preparationsof Intermediates and preparation of accompanying Examples.

Synthetic Scheme(s)

Scheme 1 illustrates an exemplary preparation of C-1. Reacting asolution of amine A-1, and acid B-1 with a coupling agent such as T3P,EDCI/HOBt, in the presence of a base such as TEA, DMAP and DIEA, andsolvent such as DMF and DCM, affords C-1.

In Scheme 1, examples of A include a substituted or unsubstituted alkyland a substituted or unsubstituted cycloalkyl, examples of B include awarhead moiety, such as cyano, aldehyde, hydroxymethylketone, ketoamide,heteroaryl-ketone, enone, and Michael acceptor warhead, examples of Cinclude an alkyl substituted with a 4-, 5-, or 6-membered lactam, andexamples of D include a substituted or unsubstituted bicyclic heteroarylmoiety. In Scheme 1, exemplary preparation of a cyano moiety at Binclude a dehydration of an amide to nitrile with a dehydration agentsuch as Burgess reagent.

Compounds of Table 1 have been prepared following general Scheme 1,which follows the examples described below, such as examples 19, 25, 27,32, 39, and 41.

Example 1. Synthesis of Viral Protease Inhibitor Compound 103

Step 1:(2S)-2-[[(2S)-2-(1H-benzimidazole-2-carbonylamino)-4-methyl-pentanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate

To a mixture of methyl(2S)-2-[[(2S)-2-amino-4-methyl-pentanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(200 mg, 483.81 umol, 1 eq, TFA) and 1H-benzimidazole-2-carboxylic acid(94.14 mg, 580.57 umol, 1.2 eq) in DCM (2 mL) was added EDCI (185.49 mg,967.61 umol, 2 eq) and DMAP (118.21 mg, 967.61 umol, 2 eq). The mixturewas added DMF (1 mL) and stirred at 25° C. for 4 h. The resultingmixture was diluted with H₂O (20 mL) and extracted with DCM (10 mL*3).The combined organic layers were dried over Na₂SO₄, filtered andconcentrated under reduced pressure to give a residue. The residue waspurified by prep-TLC (SiO₂, DCM/MeOH=5/1), to give methyl(2S)-2-[[(2S)-2-(1H-benzimidazole-2-carbonylamino)-4-methyl-pentanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(150 mg, 338.22 umol) as a solid.

Step 2: N-[(1S)-3-methyl-1-[[(1S)-1-(nitrosomethyl)-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]carbamoyl]butyl]-1H-benzimidazole-2-carboxamide

Methyl(2S)-2-[[(2S)-2-(1H-benzimidazole-2-carbonylamino)-4-methyl-pentanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(150 mg, 338.22 umol, 1 eq) was added NH₃/MeOH (7 M, 5 mL, 103.48 eq).The mixture was stirred at 80° C. for 16 h in a sealed tube. Thereaction was concentrated in vacuo to dryness, give compoundN-[(1S)-3-methyl-1-[[(1S)-1-(nitrosomethyl)-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]carbamoyl]butyl]-1H-benzimidazole-2-carboxamide(140 mg, crude) as a solid. The crude product was used directly in nextstep.

Step 3:N-[(1S)-1-[[(1S)-1-cyano-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]carbamoyl]-3-methyl-butyl]-1H-benzimidazole-2-carboxamide

N-[(1S)-3-methyl-1-[[(1S)-1-(nitrosomethyl)-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]carbamoyl]butyl]-1H-benzimidazole-2-carboxamide(120.00 mg, 280.06 umol, 1 eq) in DCM (5 mL) was added Burgess reagent(150 mg, 629.45 umol, 2.25 eq). The mixture was stirred at 25° C. for 4h. The reaction was blow-dried under N₂. The residue was purified byprep-HPLC (column: Waters Xbridge Prep OBD C18 150*40 mm*10 um; mobilephase: [water (10 mM NH4HCO3)-ACN]; B %: 20%-40%, 8 min), giveN-[(1S)-1-[[(1S)-1-cyano-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]carbamoyl]-3-methyl-butyl]-1H-benzimidazole-2-carboxamide(40 mg, 97.45 umol) was obtained as a solid. MS (ESI) m/z 411.1 [M+H]⁺,¹H NMR (400 MHz, DMSO-d₆) δ ppm 13.11 (br s, 1H), 8.97-8.81 (m, 2H),7.90-7.64 (m, 2H), 7.54 (br s, 1H), 7.31 (br s, 2H), 5.08-4.93 (m, 1H),4.62-4.43 (m, 1H), 3.19-3.05 (m, 2H), 2.44-2.29 (m, 1H), 2.23-2.05 (m,2H), 1.91-1.50 (m, 5H), 0.91 (dd, J=6.3, 8.9 Hz, 6H).

Example 2. Synthesis of Viral Protease Inhibitor Compound 105

Step 1:(2S)-2-[[(2S)-4-methyl-2-(2-naphthylsulfonylamino)pentanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate

To a mixture of methyl(2S)-2-[[(2S)-2-amino-4-methyl-pentanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(150 mg, 501.06 umol, 1 eq) in DMF (5 mL) was addednaphthalene-2-sulfonyl chloride (227.16 mg, 1.00 mmol, 2 eq) and DMAP(155.35 mg, 1.27 mmol, 2.54 eq) and stirred at 25° C. Then the reactionwas stirred at 80° C. for 16 h. The reaction mixture was diluted withH₂O (20 mL) and extracted with EtOAc (10 mL*3). The combined organiclayers were dried over Na₂SO₄, filtered and concentrated under reducedpressure to give a residue. The residue was purified by prep-TLC (SiO₂,DCM/MeOH=10/1). Give methyl(2S)-2-[[(2S)-4-methyl-2-(2-naphthylsulfonylamino)pentanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(70 mg, 142.98 umol) as an oil.

Step 2:(2S)—N-[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]-4-methyl-2-(2-naphthylsulfonylamino)pentanamide

To a mixture of methyl(2S)-2-[[(2S)-4-methyl-2-(2-naphthylsulfonylamino)pentanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(50 mg, 102.13 umol, 1 eq) was added NH₃/MeOH (7 M, 10 mL, 685.42 eq)and stirred at 80° C. for 16 h. The reaction was concentrated in vacuoto dryness to give the crude of(2S)—N-[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]-4-methyl-2-(2-naphthylsulfonylamino)pentanamide(50 mg, crude) as an oil.

Step 3: (2S)—N-[(1S)-1-cyano-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]-4-methyl-2-(2-naphthylsulfonylamino)pentanamide

(2S)—N-[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]-4-methyl-2-(2-naphthylsulfonylamino)pentanamide(70 mg, 147.50 umol, 1 eq) in DCM (0.5 mL) was added Burgess reagent(79.00 mg, 331.52 umol, 2.25 eq). The mixture was stirred at 25° C. for4 h. The reaction was blow-dried under N₂. The residue was purified byprep-HPLC: column: Waters Xbridge Prep OBD C18 150*40 mm*10 um; mobilephase: [water (10 mM NH₄HCO₃)-ACN]; B %: 25%-55%, 8 min, give compound(2S)—N-[(1S)-1-cyano-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]-4-methyl-2-(2-naphthylsulfonylamino)pentanamide(30 mg, 65.71 umol) as a solid. MS (ESI) m/z 457.1 [M+H]⁺. ¹H NMR (400MHz, DMSO-d₆) δ ppm 8.81 (br d, J=7.5 Hz, 1H), 8.38 (s, 1H), 8.21 (br s,1H), 8.12-8.03 (m, 2H), 8.00 (d, J=7.7 Hz, 1H), 7.82-7.72 (m, 1H),7.71-7.56 (m, 3H), 4.64 (q, J=7.6 Hz, 1H), 3.78-3.67 (m, 1H), 3.09-3.01(m, 1H), 3.00-2.89 (m, 1H), 2.08-1.96 (m, 1H), 1.90-1.78 (m, 1H),1.71-1.60 (m, 1H), 1.58-1.33 (m, 4H), 1.31-1.19 (m, 1H), 0.78 (d, J=6.6Hz, 3H), 0.63 (d, J=6.6 Hz, 3H).

Example 3. Synthesis of benzylN-[(1S)-1-[[(1S)-1-cyano-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]carbamoyl]-3-methyl-butyl]carbamate

Step 1: methyl (2S)-2-amino-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate

To a mixture of methyl(2S)-2-(tert-butoxycarbonylamino)-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate (300 mg, 1.05 mmol, 1 eq) in DCM (5 mL) was added TFA (4.62g, 40.52 mmol, 3 mL, 38.67 eq), then the mixture was stirred at 25° C.for 2 h. Once the reaction was completed, the reaction mixture wasconcentrated under reduced pressure to give a residue and used nextstep. Compound methyl(2S)-2-amino-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate (180 mg, 918.33umol) was obtained as a colorless oil. MS (ESI) m/z 187.1 [M+H]⁺

Step 2: methyl(2S)-2-[[(2S)-2-(tert-butoxycarbonylamino)-4-methyl-pentanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate

To a mixture of methyl(2S)-2-amino-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate (189.47 mg, 966.66umol) and (2S)-2-(benzyloxycarbonylamino)-4-methyl-pentanoic acid(256.46 mg, 966.66 umol, 1 eq) in DCM (2 mL) was added DMAP (236.19 mg,1.93 mmol, 2 eq) and EDCI (370.62 mg, 1.93 mmol, 2 eq). The mixture wasadded with DMF (1 mL) and stirred at 25° C. for 14 h. Once the reactionwas completed, the reaction mixture was diluted with H₂O (50 mL) andextracted with DCM (30 mL*3). The combined organic layers were washedwith brine (50 mL), dried over Na₂SO₄, filtered and concentrated underreduced pressure to give a residue. The residue was purified by columnchromatography (SiO₂, petroleum ether/EtOAc=3/1 to 0/1) to get thecompound methyl(2S)-2-[[(2S)-2-(benzyloxycarbonylamino)-4-methyl-pentanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(250 mg, 461.36 umol) as a solid. MS (ESI) m/z 434.3 [M+H]⁺

Step 3: benzylN-[(1S)-1-[[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]carbamoyl]-3-methyl-butyl]carbamate

Methyl(2S)-2-[[(2S)-2-(benzyloxycarbonylamino)-4-methyl-pentanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(200 mg, 369.09 umol, 1 eq) was added NH₃/MeOH (7 M, 58.14 mL, 1102.58eq). The mixture was stirred at 80° C. for 16 h. Once the reaction wascompleted, the reaction mixture was concentrated under reduced pressureto give a residue and used directly next step. Compound benzylN-[(1S)-1-[[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]carbamoyl]-3-methyl-butyl]carbamate (150 mg, 322.59 umol)was obtained as a colorless oil.

Step 4: benzylN-[(1S)-1-[[(1S)-1-cyano-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]carbamoyl]-3-methyl-butyl]carbamate

To a mixture of benzylN-[(1S)-1-[[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]carbamoyl]-3-methyl-butyl]carbamate (150 mg, 179.22 umol, 1 eq) in DCM(5 mL) was added Burgess reagent (42.71 mg, 179.22 umol, 1 eq). Themixture was stirred at 25° C. for 1 h. Once the reaction was completed,the reaction mixture was concentrated under reduced pressure to give aresidue. The residue was purified by neutral prep-HPLC (column:WatersXbridge BEH C18 100*30 mm*10 um; mobile phase: [water (10 mMNH₄HCO₃)-ACN]; B %: 20%-50%, 8 min) to get the compound benzylN-[(1S)-1-[[(1S)-1-cyano-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]carbamoyl]-3-methyl-butyl]carbamate(28 mg, 69.92 umol) as a solid. MS (ESI) m/z 401.1 [M+H]⁺. ¹H NMR (400MHz, DMSO-d₆) δ ppm 8.84 (br d, J=7.9 Hz, 1H), 7.70 (s, 1H), 7.54 (br d,J=7.8 Hz, 1H), 7.41-7.24 (m, 5H), 5.02 (s, 2H), 4.97-4.88 (m, 1H),4.07-3.91 (m, 1H), 3.20-2.94 (m, 2H), 2.38-2.22 (m, 1H), 2.22-1.98 (m,2H), 1.85-1.26 (m, 5H), 0.87 (br dd, J=6.5, 11.2 Hz, 6H)

Example 4. Synthesis of Viral Protease Inhibitor Compound 131

Step 1:(2S)-2-[[(2S)-2-(1H-imidazo[4,5-b]pyridine-2-carbonylamino)-4-methyl-pentanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate

To a mixture of methyl(2S)-2-[[(2S)-2-amino-4-methyl-pentanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(250 mg, 604.76 umol, 1 eq, TFA) and1H-imidazo[4,5-b]pyridine-2-carboxylic acid (118.39 mg, 725.71 umol, 1.2eq) in DCM (4 mL) was added EDCI (231.86 mg, 1.21 mmol, 2 eq) and DMAP(147.77 mg, 1.21 mmol, 2 eq). The mixture was added with DMF (2 mL) andstirred at 25° C. for 4 h. The reaction mixture was diluted with H₂O (20mL) and extracted with DCM (30 mL). The combined organic layers weredried over Na₂SO₄, filtered and concentrated under reduced pressure togive a residue. The residue was purified by prep-TLC (SiO₂,DCM/MeOH=5/1) to give compound methyl(2S)-2-[[(2S)-2-(1H-imidazo[4,5-b]pyridine-2-carbonylamino)-4-methyl-pentanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(100 mg, 224.98 umol) as a solid.

Step 2:N-[(1S)-1-[[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]carbamoyl]-3-methyl-butyl]-1H-imidazo[4,5-b]pyridine-2-carboxamide

To a mixture of methyl(2S)-2-[[(2S)-2-(1H-imidazo[4,5-b]pyridine-2-carbonylamino)-4-methyl-pentanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(100 mg, 224.98 umol, 1 eq) was added NH₃/MeOH (7 M, 27.54 mL, 856.77eq) and stirred at 80° C. for 16 h. The reaction was concentrated invacuo to dryness to give the crude ofN-[(1S)-1-[[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]carbamoyl]-3-methyl-butyl]-1H-imidazo[4,5-b]pyridine-2-carboxamide(90 mg, crude) as an oil.

Step 3: N-[(1S)-1-[[(1S)-1-cyano-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]carbamoyl]-3-methyl-butyl]-H-imidazo[4,5-b]pyridine-2-carboxamide

N-[(1S)-1-[[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]carbamoyl]-3-methyl-butyl]-1H-imidazo[4,5-b]pyridine-2-carboxamide(80 mg, 186.28 umol, 1 eq) in DCM (3 mL) was added Burgess reagent(100.00 mg, 419.62 umol, 2.25 eq). The mixture was stirred at 25° C. for4 h. The reaction was blow-dried under N₂. The residue was purified byprep-HPLC (column: Waters Xbridge Prep OBD C18 150*40 mm*10 um; mobilephase: [water (10 mM NH4HCO3)-ACN]; B %: 10%-35%, 8 min) to giveN-[(1S)-1-[[(1S)-1-cyano-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]carbamoyl]-3-methyl-butyl]-1H-imidazo[4,5-b]pyridine-2-carboxamide(25 mg, 60.76 umol) as a solid. MS (ESI) m/z 412.1 [M+H]⁺. ¹H NMR (400MHz, DMSO-d₆) δ ppm 13.58 (br s, 1H), 9.29-8.96 (m, 1H), 8.89 (d, J=7.9Hz, 1H), 8.49 (br s, 1H), 8.28-7.84 (m, 1H), 7.71 (s, 1H), 7.36 (dd,J=4.6, 8.2 Hz, 1H), 5.06-4.93 (m, 1H), 4.61-4.44 (m, 1H), 3.20-3.06 (m,2H), 2.43-2.31 (m, 1H), 2.20-2.07 (m, 2H), 1.90-1.53 (m, 5H), 0.92 (dd,J=6.4, 9.5 Hz, 6H).

Example 5. Synthesis of Viral Protease Inhibitor Compound 121

Step 1:(2S)-2-(tert-butoxycarbonylamino)-3-[(3S)-2-oxopyrrolidin-3-yl]propanoicacid

To a mixture of methyl(2S)-2-(tert-butoxycarbonylamino)-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate (1.2 g, 3.77 mmol) in THF (3 mL), ACN (3 mL) and H₂O (3 mL)was added LiOH.H₂O (158.29 mg, 3.77 mmol, 1 eq). The mixture was stirredat 25° C. for 2 h. Once the reaction was completed, the solution wasconcentrated to give a residue, and then the residue was adjusted topH˜4 with HCl. The resulting residue was extracted with EtOAc (20 mL*3)and brine (20 mL), and then concentrated to give a residue compound(2S)-2-(tert-butoxycarbonylamino)-3-[(3S)-2-oxopyrrolidin-3-yl]propaneicacid (1 g, 3.31 mmol) was obtained as an oil. MS (ESI) m/z 217.1[M+H−56]⁺.

Step 2: tert-butylN-[(1S)-2-[methoxy(methyl)amino]-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]carbamate

To a mixture of(2S)-2-(tert-butoxycarbonylamino)-3-[(3S)-2-oxopyrrolidin-3-yl]propanoicacid (1.0 g, 3.31 mmol) in DCM (20 mL) was added CDI (535.94 mg, 3.31mmol, 1 eq). The mixture was stirred at 0° C. for 30 min, then addedwith DIEA (512.61 mg, 3.97 mmol, 690.85 uL, 1.2 eq) andN,O-DIMETHYLHYDROXYLAMINE HYDROCHLORIDE (322.40 mg, 3.31 mmol, 1 eq).The resulting mixture was stirred at 25° C. for 3 h. Once the reactionwas complete, the reaction mixture was diluted with H₂O (30 mL) andextracted with ethyl acetate (30 mL*3). The combined organic layers werewashed with brine (30 mL), dried over Na₂SO₄, filtered and concentratedunder reduced pressure to give a residue. The residue was purified bycolumn chromatography (SiO₂, petroleum ether/EtOAc=5/1 to 0/1) to getthe compound tert-butylN-[(1S)-2-[methoxy(methyl)amino]-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]carbamate(0.9 g, 2.57 mmol) which was obtained as an oil. MS (ESI) m/z 316.2[M+H]⁺

Step 3: tert-butylN-[(1S)-2-(1,3-benzothiazol-2-yl)-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]carbamate

To a mixture of 2-bromo-1,3-benzothiazole (458.22 mg, 2.14 mmol, 1.5 eq)in THF (20 mL) was added n-BuLi (2.5 M, 684.92 uL, 1.2 eq) in oneportion at −78° C. under N₂. The mixture was stirred at −78° C. for 30min, and then added with tert-butylN-[(1S)-2-[methoxy(methyl)amino]-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]carbamate(500 mg, 1.43 mmol) at −78° C. The resulting mixture was stirred for 1hour, and then the reaction mixture was quenched by the addition ofNH₄Cl (10 mL) at 0° C., and then stirred for 10 min at 0° C. Theresulting mixture was diluted with water (100 mL) and extracted withEtOAc (50 mL*3). The combined organic layers were washed with brine (50mL), dried over Na₂SO₄, filtered and concentrated under reduced pressureto give a residue. The residue was purified by MPLC (SiO₂, petroleumether/EtOAc-MeOH=10/1 to 0/1) to get the compound tert-butylN-[(1S)-2-(1,3-benzothiazol-2-yl)-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]carbamate (150 mg, 346.63 umol) as a colorless oil. MS(ESI) m/z 390.1 [M+H]⁺

Step 4:(3S)-3-[(2S)-2-amino-3-(1,3-benzothiazol-2-yl)-3-oxo-propyl]pyrrolidin-2-one

To a mixture of tert-butylN-[(1S)-2-(1,3-benzothiazol-2-yl)-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]carbamate (150 mg, 346.63 umol) was added HCl/EtOAc (4 M,86.66 uL, 1 eq). The resulting mixture was stirred at 20° C. for 2 h,and then concentrated under reduced pressure to give a residue(3S)-3-[(2S)-2-amino-3-(1,3-benzothiazol-2-yl)-3-oxo-propyl]pyrrolidin-2-one (100 mg, crude) as anoil which was directly used in the next step. MS (ESI) m/z 290.1 [M+H]⁺

Step 5:N-[(1S)-1-[[(1S)-2-(1,3-benzothiazol-2-yl)-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide

To a mixture of(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4-methyl-pentanoic acid(18.93 mg, 62.21 umol, 1 eq) in DMF (1 mL) was added 1-methylimidazole(25.54 mg, 311.04 umol, 24.79 uL, 5 eq) and[chloro(dimethylamino)methylene]-dimethyl-ammonium hexafluorophosphate(20.95 mg, 74.65 umol, 1.2 eq) at 0° C. The resulting mixture wasstirred at 0° C. for 30 min, and then added with(3S)-3-[(2S)-2-amino-3-(1,3-benzothiazol-2-yl)-3-oxo-propyl]pyrrolidin-2-one(18 mg, 62.21 umol, 1 eq). The resulting mixture was stirred at 25° C.for 2 h. Once the reaction was completed, the reaction mixture wasfiltered and concentrated under reduced pressure to give a residue. Thecrude was purified by neutral prep-HPLC (column: Waters Xbridge BEH C18100*30 mm*10 um; mobile phase: [water (10 mM NH4HCO3)-ACN]; B %:35%-65%, 10 min) and SFC (column: DAICEL CHIRALCEL OX (250 mm*30 mm, 10um); mobile phase: [0.1% NH₃H₂O MEOH]; B %: 50%-50%, 12 min) separationto get the compoundN-[(1S)-1-[[(1S)-2-(1,3-benzothiazol-2-yl)-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide(8 mg, 13.48 umol) as a solid. MS (ESI) m/z 576.3 [M+H]⁺. ¹H NMR (400MHz, DMSO-d₆) δ=11.69 (s, 1H), 8.75-8.51 (m, 2H), 8.08 (d, J=7.9 Hz,1H), 7.95 (d, J=8.2 Hz, 1H), 7.68 (s, 1H), 7.50 (t, J=7.4 Hz, 1H),7.44-7.37 (m, 1H), 7.19-7.07 (m, 4H), 6.93 (d, J=8.2 Hz, 1H), 6.49 (d,J=7.7 Hz, 1H), 3.89 (s, 3H), 3.15-2.99 (m, 2H), 2.46-2.30 (m, 1H),2.21-1.94 (m, 4H), 1.93-1.74 (m, 1H), 1.57-1.40 (m, 2H), 0.83-0.71 (m,6H).

Example 6. Synthesis of Viral Protease Inhibitor Compound 185

Step 1: (S)-methyl2-((S)-2-((tert-butoxycarbonyl)amino)-3-cyclohexylpropanamido)-3-((S)-2-oxopyrrolidin-3-yl)propanoate

To a solution of methyl(2S)-2-amino-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate (170 mg, 763.47umol, 1 eq, HCl) and(2S)-2-(tert-butoxycarbonylamino)-3-cyclohexyl-propanoic acid (207.17mg, 763.47 umol, 1 eq) in DMF (2 mL) was added DMAP (186.55 mg, 1.53mmol, 2 eq) and EDCI (292.71 mg, 1.53 mmol, 2 eq). The mixture was addedDCM (3 mL) and stirred at 25° C. for 2 h. LCMS showed the reaction wascompleted, and desired MS was observed. The reaction mixture wasquenched by addition H₂O (30 mL) at 0° C., and then extracted with DCM(20 mL*3). The combined organic layers were washed with brine (10 mL),dried over Na₂SO₄, filtered and concentrated under reduced pressure togive a residue. The residue was purified by prep-TLC (SiO₂, petroleumether/EtOAc=0/1) to get the product methyl(2S)-2-[[(2S)-2-(tert-butoxycarbonylamino)-3-cyclohexyl-propanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(250 mg, 568.77 umol, 74.50% yield) was obtained as a solid. MS (ESI)m/z 440.3 [M+H]⁺

Step 2: (S)-methyl2-((S)-2-amino-3-cyclohexylpropanamido)-3-((S)-2-oxopyrrolidin-3-yl)propanoate

A solution of methyl(2S)-2-[[(2S)-2-(tert-butoxycarbonylamino)-3-cyclohexyl-propanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(200 mg, 455.02 umol, 1 eq) in EtOAc (0.5 mL) was added drop-wiseHCl/EtOAc (4 M, 2.00 mL, 17.58 eq) at 25° C. The mixture was stirred at25° C. for 1 h. The reaction mixture was concentrated under reducedpressure to give a product methyl(2S)-2-[[(2S)-2-amino-3-cyclohexyl-propanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(150 mg, crude, HCl) was obtained as a solid and used directly nextstep. MS (ESI) m/z 340.1 [M+H]⁺

Step 3: ((S)-methyl2-((S)-3-cyclohexyl-2-(4-methoxy-1H-indole-2-carboxamido)propanamido)-3-((S)-2-oxopyrrolidin-3-yl)propanoate

A solution of 4-methoxy-1H-indole-2-carboxylic acid (99.18 mg, 518.77umol, 1.3 eq) and methyl(2S)-2-[[(2S)-2-amino-3-cyclohexyl-propanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(150 mg, 399.05 umol, 1 eq, HCl) in DMF (2 mL) was added DMAP (97.50 mg,798.11 umol, 2.0 eq) and EDCI (153.00 mg, 798.11 umol, 2 eq). Themixture was added DCM (4 mL) and stirred at 25° C. for 2 h. The reactionmixture was quenched by addition H₂O (20 mL) at 0° C., and thenextracted with DCM (20 mL*3). The combined organic layers were washedwith brine (20 mL), dried over Na₂SO₄, filtered and concentrated underreduced pressure to give a residue. The residue was purified by columnchromatography (SiO₂, DCM:MeOH=1:0 to 10:1) to get a product methyl(2S)-2-[[(2S)-3-cyclohexyl-2-[(4-methoxy-1H-indole-2-carbonyl)amino]propanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(150 mg, 292.63 umol, 73.33% yield) was obtained as a solid.

¹H NMR (METHANOL-d₄, 400 MHz): δ ppm 7.26 (s, 1H), 7.09-7.20 (m, 1H),7.02 (d, J=8.3 Hz, 1H), 6.51 (d, J=7.6 Hz, 1H), 4.66 (br dd, J=9.0, 6.3Hz, 1H), 4.52-4.58 (m, 1H), 3.93 (s, 3H), 3.72 (s, 3H), 3.22-3.29 (m,2H), 2.54-2.62 (m, 1H), 2.26-2.33 (m, 1H), 2.15-2.23 (m, 1H), 1.66-1.87(m, 9H), 1.47-1.54 (m, 1H), 1.25-1.40 (m, 3H), 0.96-1.06 (m, 2H)

Step 4:N—((S)-1-(((S)-1-amino-1-oxo-3-((S)-2-oxopyrrolidin-3-yl)propan-2-yl)amino)-3-cyclohexyl-1-oxopropan-2-yl)-4-methoxy-1H-indole-2-carboxamide

A solution of methyl(2S)-2-[[(2S)-3-cyclohexyl-2-[(4-methoxy-1H-indole-2-carbonyl)amino]propanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(150 mg, 292.63 umol, 1 eq) in ammonia (15.30 g, 898.39 mmol, 15.00 mL,3070.07 eq) was heated at 80° C. for 12 hours in a sealed tube. Thereaction mixture was concentrated under reduced pressure to get aproductN-[(1S)-2-[[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]amino]-1-(cyclohexylmethyl)-2-oxo-ethyl]-4-methoxy-1H-indole-2-carboxamide(140 mg, crude) was obtained as a solid. MS (ESI) m/z 498.2 [M+H]⁺

¹H NMR (METHANOL-d₄, 400 MHz): δ ppm 7.27-7.34 (m, 1H), 7.13-7.20 (m,1H), 7.05 (d, J=8.3 Hz, 1H), 6.53 (d, J=7.7 Hz, 1H), 4.62 (t, J=7.6 Hz,1H), 4.42-4.51 (m, 1H), 3.95 (s, 3H), 3.22-3.30 (m, 2H), 2.53 (td,J=9.2, 4.5 Hz, 1H), 2.33 (ddd, J=9.2, 6.4, 3.4 Hz, 1H), 2.17 (ddd,J=14.1, 11.4, 4.6 Hz, 1H), 1.71-1.88 (m, 9H), 1.46-1.53 (m, 1H),1.21-1.32 (m, 3H), 0.97-1.09 (m, 2H)

Step 5:N—((S)-1-(((S)-1-amino-1-oxo-3-((S)-2-oxopyrrolidin-3-yl)propan-2-yl)amino)-3-cyclohexyl-1-oxopropan-2-yl)-4-methoxy-1H-indole-2-carboxamide

To a solution ofN-[(1S)-2-[[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]amino]-1-(cyclohexylmethyl)-2-oxo-ethyl]-4-methoxy-1H-indole-2-carboxamide(80 mg, 160.78 umol, 1 eq) in DCM (3 mL) was added Burgess reagent(114.94 mg, 482.33 umol, 3 eq), and then the resulting mixture wasstirred at 25° C. for 3 h. The reaction mixture was concentrated underreduced pressure to give a residue. The residue was purified by neutralprep-HPLC to give a productN-[(1S)-2-[[(1S)-1-cyano-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]amino]-1-(cyclohexylmethyl)-2-oxo-ethyl]-4-methoxy-1H-indole-2-carboxamide(20.02 mg, 41.75 umol) was obtained as a solid. MS (ESI) m/z 480.1[M+H]⁺.

Prep-HPLC condition: column: Waters Xbridge BEH C18 100*25 mm*5 um;mobile phase: [water (10 mM NH₄HCO₃)-ACN]; B %: 30%-60%, 10 min

¹H NMR (METHANOL-d₄, 400 MHz): δ ppm 7.28 (s, 1H), 7.11-7.18 (m, 1H),7.02 (d, J=8.3 Hz, 1H), 6.51 (d, J=7.6 Hz, 1H), 5.05 (dd, J=10.1, 5.9Hz, 1H), 4.56-4.61 (m, 1H), 3.93 (s, 3H), 3.22-3.30 (m, 2H), 2.55-2.66(m, 1H), 2.23-2.40 (m, 2H), 1.65-1.94 (m, 9H), 1.41-1.52 (m, 1H),1.17-1.36 (m, 3H), 0.94-1.10 (m, 2H).

Example 7. Synthesis of Viral Protease Inhibitor Compound 101

Step 1: Methyl (2S)-2-amino-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate;hydrochloride

Methyl(2S)-2-(tert-butoxycarbonylamino)-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(500 mg, 1.75 mmol, 1 eq) was added HCl/EtOAc (4 M, 10 mL, 22.91 eq) at25° C. The mixture was stirred at 25° C. for 0.5 h. The resultingmixture was concentrated under reduced pressure to give a product methyl(2S)-2-amino-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate; hydrochloride (300mg, 1.28 mmol, 73.29% yield, 95% purity) as a solid and used directlynext step. MS (ESI) m/z 187.1 [M+H]⁺

Step 2: methyl(2S)-2-[[(2S)-2-(tert-butoxycarbonylamino)-4-methyl-pentanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate

To a mixture of methyl(2S)-2-amino-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate; hydrochloride(157.89 mg, 673.65 umol, 95% purity, 1 eq) and(2S)-2-(tert-butoxycarbonylamino)-4-methyl-pentanoic acid (155.81 mg,673.65 umol, 1 eq) in DMF (2 mL) was added EDCI (258.28 mg, 1.35 mmol, 2eq) and DMAP (164.60 mg, 1.35 mmol, 2 eq). The mixture was added DCM (3mL) and stirred at 25° C. for 14 h. The resulting mixture was dilutedwith H₂O (50 mL) and extracted with DCM (30 mL*3). The combined organiclayers were washed with brine, dried over Na₂SO₄, filtered andconcentrated under reduced pressure to give a residue. The residue waspurified by column chromatography (SiO2, petroleum ether/EtOAc=3/1 to1/1) to get the product methyl(2S)-2-[[(2S)-2-(tert-butoxycarbonylamino)-4-methyl-pentanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(250 mg, 500.65 umol, 74.32% yield, 80% purity) was obtained as a solid.MS (ESI) m/z 400.3 [M+H]⁺

Step 3:(2S)-2-amino-N-[(1S)-1-cyano-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]-4-methyl-pentanamide

tert-butylN-[(1S)-1-[[(1S)-1-cyano-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]carbamoyl]-3-methyl-butyl]carbamate (200 mg, 491.19 umol, 90% purity, 1 eq) in DCM (5 mL) wasadded TFA (770.00 mg, 6.75 mmol, 0.5 mL, 13.75 eq) at 25° C. The mixturewas stirred at 25° C. for 1 h. The resulting mixture was concentratedunder reduced pressure to give a product(2S)-2-amino-N-[(1S)-1-cyano-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]-4-methyl-pentanamide (120 mg, 405.50 umol, 82.55% yield, 90%purity) as an oil and used directly next step. MS (ESI) m/z 300.2 [M+H]⁺

Step 4:methyl(2S)-2-[[(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4-methyl-pentanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate

To a mixture of 4-methoxy-1H-indole-2-carboxylic acid (120 mg, 627.67umol, 1 eq) and methyl(2S)-2-[[(2S)-2-amino-4-methyl-pentanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(208.78 mg, 627.67 umol, 90% purity, 1 eq) in DCM (1 mL) was added EDCI(240.65 mg, 1.26 mmol, 2 eq) and DMAP (153.36 mg, 1.26 mmol, 2 eq). Themixture was added DMF (0.5 mL) and stirred at 25° C. for 14 h. Theresulting mixture was diluted with H₂O (50 mL) and extracted with DCM(30 mL*3). The combined organic layers were washed with brine (50 mL),dried over Na₂SO₄, filtered and concentrated under reduced pressure togive a residue. The residue was purified by column chromatography (SiO2,petroleum ether/EtOAc=3/1 to 0/1) to get the compoundmethyl(2S)-2-[[(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4-methyl-pentanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate (160 mg, 304.74 umol,48.55% yield, 90% purity) as a solid. MS (ESI) m/z 473.3 [M+H]⁺

Step 5:N-[(1S)-1-[[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide

methyl(2S)-2-[[(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4-methyl-pentanoyl]amino]3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(180 mg, 342.83 umol, 90% purity, 1 eq) was added NH₃/MeOH (7 M, 54.00mL, 1102.58 eq), The mixture was stirred at 80° C. for 16 h. Theresulting mixture was concentrated under reduced pressure to give aresidueN-[(1S)-1-[[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide(130 mg, 255.73 umol, 74.59% yield, 90% purity) as an oil. MS (ESI) m/z458.3 [M+H]⁺

1H NMR (400 MHz, METHANOL-d4) δ ppm 0.97-1.02 (dd, J=14.55, 6.11 Hz, 6H)1.74-1.82 (m, 5H) 2.15 (ddd, J=14.03, 11.34, 4.58 Hz, 1H) 2.25-2.37 (m,1H) 2.52 (ddt, J=13.82, 9.41, 4.71, 4.71 Hz, 1H) 3.17-3.29 (m, 2H) 3.90(s, 3H) 4.46 (dd, J=11.25, 4.16 Hz, 1H) 4.60 (dd, J=9.66, 5.01 Hz, 1H)6.50-6.52 (d, J=7.70 Hz, 1H) 7.02-7.04 (d, J=8.31 Hz, 1H) 7.15-7.17 (m,1H) 7.28-7.29 (d, J=0.73 Hz, 1H)

Step 6:N-[(1S)-1-[[(1S)-1-cyano-2-1(3S)-2-oxopyrrolidin-3-yl]ethyl]carbamoyl-3-methyl-butyl-4-methoxy-1H-indole-2-carboxamide

To a mixture ofN-[(1S)-1-[[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide (100 mg,196.71 umol, 90% purity, 1 eq) in DCM (4 mL) was added Burgess reagent(93.75 mg, 393.42 umol, 2 eq). The mixture was stirred at 25° C. for 1h. The resulting mixture was concentrated under reduced pressure to givea residue. The residue was purified by neutral prep-HPLC to get theproductN-[(1S)-1-[[(1S)-1-cyano-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide(23 mg, 49.50 umol, 25.16% yield, 94.59% purity) as a solid. MS (ESI)m/z 440.1 [M+H]⁺.

Prep-HPLC condition:

column:Waters Xbridge BEH C18 100*30 mm*10 um; mobile phase: [water (10mM NH4HCO3)-ACN]; B %: 27%-57%, 10 min

1H NMR (400 MHz, DMSO-d6) δ ppm 0.88-0.94 (m, 6H) 1.67-1.74 (m, 5H)2.11-2.13 (m, 2H) 2.14-2.34 (m, 1H) 3.09-3.14 (m, 2H) 3.88 (s, 3H)4.36-4.57 (m, 1H) 4.90-5.00 (m, 1H) 6.49-6.51 (d, J=7.58 Hz, 1H)6.99-7.01 (m, 2H) 7.38 (s, 1H) 7.70 (s, 1H) 8.45-8.47 (br d, J=7.70 Hz,1H) 8.89-8.91 (br d, J=7.95 Hz, 1H) 11.57 (br s, 1H)

Example 8. Synthesis of Viral Protease Inhibitor Compound 593

Step 1: methyl (2S)-2-amino-3-(1H-imidazol-5-yl) propanoate

To the solution of(2S)-2-(tert-butoxycarbonylamino)-3-(1H-imidazol-5-yl)propanoic acid(0.5 g, 1.96 mmol, 1 eq) in MeOH (0.6 mL) was added HCl/MeOH (4 M, 4.90mL, 10 eq) at 25° C. The reaction mixture was stirred at 25° C. for 12h. The reaction mixture was concentrated to get the product. Methyl(2S)-2-amino-3-(1H-imidazol-5-yl) propanoate (400 mg, crude, HCl) wasobtained as a solid and used directly next step. MS (ESI) m/z 170.1[M+H]⁺

Step 2: methyl(2S)-3-(1H-imidazol-5-yl)-2-[[(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4-methyl-pentanoyl]amino]propanoate

To a mixture of(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4-methyl-pentanoic acid(741.86 mg, 1.77 mmol, 1 eq, TFA) and methyl(2S)-2-amino-3-(1H-imidazol-5-yl)propanoate (0.3 g, 1.77 mmol, 1 eq,HCl), DIPEA (1.15 g, 8.87 mmol, 1.54 mL, 5 eq) in THF (0.3 mL) and DCM(0.3 mL) was added T3P (1.69 g, 2.66 mmol, 1.58 mL, 50% purity, 1.5 eq)at 0° C. under N₂. The mixture was stirred at 25° C. for 12 h. Thereaction mixture was added saturated sodium bicarbonate solution (10 mL)and extracted with DCM (10 mL*2) to get the organic phase. The organicphase was washed with brine (3 mL*3) and dried over anhydrous sodiumsulfate and concentrated to get the crude product. Methyl(2S)-3-(1H-imidazol-5-yl)-2-[[(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4-methyl-pentanoyl]amino]propanoate(300 mg, crude) was obtained as a solid and used directly next step. MS(ESI) m/z 456.2 [M+H]⁺

1H NMR (400 MHz, METHANOL-d₄) δ ppm 7.48 (s, 1H), 7.27 (s, 1H),7.11-7.18 (m, 1H), 7.02 (d, J=8.16 Hz, 1H), 6.85 (s, 1H), 6.51 (d,J=7.72 Hz, 1H), 4.60-4.71 (m, 2H), 3.93 (s, 3H), 3.68 (s, 3H), 3.00-3.17(m, 3H), 1.62-1.78 (m, 3H), 0.97 (dd, J=13.78, 6.06 Hz, 6H)

Step 3: N-[(1S)-1-[[(1S)-2-amino-1-(1H-imidazol-5-ylmethyl)-2-oxo-ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide

To methyl(2S)-3-(1H-imidazol-5-yl)-2-[[(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4-methyl-pentanoyl]amino]propanoate(200 mg, 439.07 umol, 1 eq) was added NH₃/MeOH (7 M, 11.76 mL, 187.56eq) in one portion at 25° C. under N₂. The mixture was stirred at 80° C.and stirred for 12 h. The reaction mixture was cooled to 25° C. andconcentrated to get the crude product.N-[(1S)-1-[[(1S)-2-amino-1-(1H-imidazol-5-ylmethyl)-2-oxo-ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide(170 mg, 378.83 umol, 86.28% yield, 98.16% purity) was obtained as asolid and used directly next step. MS (ESI) m/z 441.2 [M+H]⁺

Step 4: N-[(1 S)-1-[[(1S)-1-cyano-2-(1H-imidazol-5-yl)ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide

To a mixture ofN-[(1S)-1-[[(1S)-2-amino-1-(1H-imidazol-5-ylmethyl)-2-oxo-ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide(140 mg, 317.82 umol, 1 eq) in DCM (2 mL) was added TFAA (133.51 mg,635.65 umol, 88.41 uL, 2 eq) at 25° C. under N₂. The mixture was stirredat 25° C. for 2 h. The reaction mixture was concentrated to get thecrude product. Crude product turned into compound 593 after 36 h instorage. The residue was purified by prep-HPLC.N-[(1S)-1-[[(1S)-1-cyano-2-(1H-imidazol-5-yl)ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide(23.89 mg, 56.31 umol, 17.72% yield, 99.581% purity) was obtained as asolid. MS (ESI) m/z 423.2 [M+H]⁺

Prep-HPLC condition:column: Waters Xbridge BEH C18 100*25 mm*5 um; mobile phase: [water (10mM NH₄HCO₃)-ACN]; B %: 25%-55%, 10 min

¹H NMR (400 MHz, METHANOL-d₄) δ ppm 7.58 (s, 1H), 7.30 (s, 1H),7.12-7.21 (m, 1H), 6.99-7.09 (m, 2H), 6.52 (d, J=7.72 Hz, 1H), 5.05 (t,J=7.06 Hz, 1H), 4.61 (br dd, J=9.70, 4.85 Hz, 1H), 3.94 (s, 3H),3.06-3.21 (m, 2H), 1.60-1.83 (m, 3H), 0.99 (dd, J=13.89, 6.17 Hz, 6H)

Step 5: tert-butyl(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)aminol-4-methyl-pentanoate

To a mixture of 4-methoxy-1H-indole-2-carboxylic acid (5 g, 26.15 mmol,1 eq) and tert-butyl (2S)-2-amino-4-methyl-pentanoate (5.88 g, 31.38mmol, 1.2 eq, HCl), EDCI (6.52 g, 34.00 mmol, 1.3 eq), HOBt (4.59 g,34.00 mmol, 1.3 eq) in DMF (30 mL) was added TEA (7.94 g, 78.46 mmol,10.92 mL, 3 eq) in one portion at 25° C. under N₂. The mixture wasstirred at 25° C. and stirred for 2 h. The reaction mixture was addedwater (90 mL) and extracted with EtOAc (25 mL*3) to get the organicphase. The organic phase was washed with 5% citric acid (25 mL) and 5%aqueous solution of sodium bicarbonate (25 mL) and dried over anhydroussodium sulfate, filtered and concentrated to get the product. Theresidue was purified by column chromatography (SiO₂, petroleumether:EtOAc=30:1 to 10:1). Tert-butyl(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4-methyl-pentanoate (5.93g, 16.45 mmol, 62.91% yield) was obtained as a solid. MS (ESI) m/z 361.2[M+H]⁺

¹H NMR (400 MHz, CHLOROFORM-d) δ ppm 9.25 (br s, 1H), 7.10-7.16 (m, 1H),6.93-7.00 (m, 2H), 6.56 (br d, J=8.31 Hz, 1H), 6.44 (d, J=7.70 Hz, 1H),4.66 (td, J=8.50, 5.14 Hz, 1H), 3.88 (s, 3H), 1.62-1.75 (m, 2H),1.57-1.62 (m, 1H), 1.42 (s, 9H), 0.92 (dd, J=6.17, 3.85 Hz, 6H).

Step 6:(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4-methyl-pentanoic acid

To a mixture of tert-butyl(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4-methyl-pentanoate (2.00g, 5.55 mmol, 1 eq) in DCM (8 mL) was added TFA (10.27 g, 90.04 mmol,6.67 mL, 16.23 eq) and H₂O (666.67 mg, 37.01 mmol, 666.67 uL, 6.67 eq)in one portion at 0° C. under N₂. The mixture was stirred at 25° C. andstirred for 4 h. The reaction mixture was concentrated to get the crudeproduct.(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4-methyl-pentanoic acid(2.24 g, 5.35 mmol, 96.50% yield, TFA) was obtained as a solid and useddirectly next step. MS (ESI) m/z 305.1 [M+H]⁺

Example 9. Synthesis of Viral Protease Inhibitor Compounds 135, 595 and136

Step 1: N-[(1S)-1-[[(1S)-1-(hydroxymethyl)-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide

To a mixture of methyl(2S)-2-[[(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4-methyl-pentanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(1.5 g, 2.86 mmol, 90% purity, 1 eq) in THF (20 mL) was added LiBH₄(124.45 mg, 5.71 mmol, 2 eq). The mixture was stirred at 25° C. for 2 h.Once the reaction was completed, the reaction mixture was quenched byaddition H₂O (10 mL) at 0° C., and extracted with EtOAc (30 mL*3). Thecombined organic layers were washed with brine (30 mL), dried overNa₂SO₄, filtered and concentrated under reduced pressure to give aresidue compoundN-[(1S)-1-[[(1S)-1-(hydroxymethyl)-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide(1.0 g, 2.25 mmol, 78.74% yield) was obtained as a solid. MS (ESI) m/z445.1 [M+H]⁺. ¹H NMR (400 MHz, METHANOL-d₄) δ=7.27 (s, 1H), 7.19-7.10(m, 1H), 7.02 (d, J=8.3 Hz, 1H), 6.51 (d, J=7.7 Hz, 1H), 4.65-4.53 (m,1H), 4.05-3.97 (m, 1H), 3.93 (s, 3H), 3.60-3.43 (m, 2H), 3.27-3.10 (m,2H), 2.59-2.43 (m, 1H), 2.39-2.19 (m, 1H), 2.08-1.89 (m, 1H), 1.85-1.63(m, 4H), 1.60-1.46 (m, 1H), 1.00 (dd, J=6.1, 12.5 Hz, 6H).

Step 2:N-[(1S)-1-[[(1S)-1-formyl-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-H-indole-2-carboxamide

To a mixture ofN-[(1S)-1-[[(1S)-1-(hydroxymethyl)-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide(674 mg, 1.52 mmol, 1 eq) in DMSO (25 mL) was added IBX (849.14 mg, 3.03mmol, 2 eq). The mixture was stirred at 25° C. for 15 h. Once thereaction was completed, the reaction mixture was diluted with H₂O (30mL) and extracted with EtOAc (30 mL*2). The combined organic layers werewashed with brine (30 mL), dried over Na₂SO₄, filtered and concentratedunder reduced pressure to give a residue. The residue was added EA (10mL) and filtered to give the productN-[(1S)-1-[[(1S)-1-formyl-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide (420 mg,759.31 umol, 50.08% yield, 80% purity) as a solid. MS (ESI) m/z 443.1[M+H]⁺. ¹H NMR (400 MHz, METHANOL-d₄) δ=7.27 (s, 1H), 7.20-7.09 (m, 1H),7.02 (d, J=8.3 Hz, 1H), 6.51 (d, J=7.7 Hz, 1H), 4.60 (dt, J=5.5, 9.9 Hz,1.5H), 4.47 (dd, J=1.4, 4.1 Hz, 0.5H), 4.02-3.94 (m, 1H), 3.93 (s, 3H),3.28-3.15 (m, 2H), 2.54-2.39 (m, 1H), 2.37-2.21 (m, 1H), 2.10-1.93 (m,1H), 1.89-1.49 (m, 5H), 1.17-0.91 (m, 6H).

Step 3:N-[(1S)-1-[[(1S)-2-cyano-2-hydroxy-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide

To a mixture ofN-[(1S)-1-[[(1S)-1-formyl-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide(400 mg, 723.15 umol, 80% purity, 1 eq) in DCM (10 mL) was addedsaturated NaHSO₃ (301.01 mg, 2.89 mmol, 203.38 uL, 4 eq). The mixturewas stirred at 25° C. for 30 min, and then an aq solution of KCN (42 mg,644.96 umol, 27.63 uL, 8.92e-1 eq) in H₂O (0.8 mL) was added. Themixture was stirred at 25° C. for 3 h. Once the reaction was completed,the organic phase was collected and the aqueous layer was extracted withDCM (30 mL*3). The combined organic phase was washed with brine (30mL*2), dried over Na₂SO₄, and concentrated to get the crude. The liquidwas added NaOH to pH=9, then quenched by adding aq NaCl, then added NaOHto pH >14. The crude was purified by HCl prep-HPLC to get the mixture120 mg, and SFC separation to get compoundN-[(1S)-1-[[(1S)-2-cyano-2-hydroxy-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide(34 mg, 70.96 umol, 9.81% yield, 97.99% purity) and compoundN-[(1S)-1-[[(1S)-2-cyano-2-hydroxy-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide(64 mg, 131.75 umol, 18.22% yield, 96.66% purity) as a solid. MS (ESI)m/z 470.2[M+H]⁺.

prep-HPLC condition: column: Phenomenex luna C18 80*40 mm*3 um; mobilephase: [water (0.04% HCl)-ACN]; B %: 26%-50%, 7 min

SFC condition: column: REGIS (R,R)WHELK-O1 (250 mm*25 mm, 10 um); mobilephase: [Neu-IPA]; B %: 35%-35%, 11 min

Compound 134 Isomer 1: ¹H NMR (400 MHz, DMSO-d₆) δ=11.57 (d, J=1.8 Hz,1H), 8.40 (d, J=7.9 Hz, 1H), 8.13 (d, J=9.3 Hz, 1H), 7.57 (s, 1H), 7.36(d, J=1.5 Hz, 1H), 7.13-7.06 (m, 1H), 7.03-6.97 (m, 1H), 6.69 (d, J=7.3Hz, 1H), 6.50 (d, J=7.7 Hz, 1H), 4.50-4.40 (m, 1H), 4.33 (t, J=7.8 Hz,1H), 4.10-3.97 (m, 1H), 3.88 (s, 3H), 3.16-2.98 (m, 2H), 2.39-2.26 (m,1H), 2.15-2.01 (m, 1H), 1.92-1.80 (m, 1H), 1.80-1.63 (m, 2H), 1.62-1.40(m, 3H), 0.90 (dd, J=6.3, 15.5 Hz, 6H).

Compound 134 Isomer 2: ¹H NMR (400 MHz, DMSO-d₆) δ=11.55 (br d, J=1.5Hz, 1H), 8.35 (d, J=7.9 Hz, 1H), 8.21 (d, J=8.6 Hz, 1H), 7.60 (s, 1H),7.34 (d, J=1.8 Hz, 1H), 7.12-7.06 (m, 1H), 7.03-6.97 (m, 1H), 6.64 (d,J=6.0 Hz, 1H), 6.50 (d, J=7.5 Hz, 1H), 4.60-4.49 (m, 2H), 4.12-3.96 (m,1H), 3.88 (s, 3H), 3.19-2.98 (m, 2H), 2.41-2.26 (m, 1H), 2.16-1.95 (m,2H), 1.92-1.35 (m, 5H), 0.98-0.82 (m, 6H).

Step 4:[(2S)-1-hydroxy-2-[[(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)aminol-4-methyl-pentanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propyl]sulfonyloxysodium

To a mixture ofN-[(1S)-1-[[(1S)-1-formyl-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide(50 mg, 112.99 umol, 1 eq) in EtOH (0.4 mL), EtOAc (0.2 mL) and H₂O (0.1mL) was added NaHSO₃ (11.76 mg, 112.99 umol, 7.94 uL, 1 eq). The mixturewas stirred at 80° C. for 16 h. Once the reaction was completed, thereaction mixture was concentrated under reduced pressure to give aresidue. The residue was added DCM (3 mL) and ACN (3 mL), filtered toget the compound[(2S)-1-hydroxy-2-[[(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4-methyl-pentanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propyl]sulfonyloxysodium (5 mg, 5.26umol, 4.66% yield, 57.5% purity) as a solid. (ESI) m/z 525.1 [M+H]⁺

¹H NMR (400 MHz, DMSO-d6) δ=11.67-11.44 (m, 1H), 9.42 (s, 0.02H),8.52-8.27 (m, 1H), 7.74-7.59 (m, 1H), 7.43 (s, 1H), 7.32 (dd, J=1.8, 4.9Hz, 1H), 7.15-6.93 (m, 2H), 6.50 (d, J=7.7 Hz, 1H), 5.40-5.24 (m, 1H),4.61-4.33 (m, 1H), 4.31-4.15 (m, 0.5H), 4.11-3.96 (m, 0.5H), 3.94 (dd,J=2.4, 5.7 Hz, 0.5H), 3.88 (s, 3H), 3.85-3.81 (m, 0.5H), 3.19-2.94 (m,2H), 2.27-1.87 (m, 3H), 1.85-1.42 (m, 5H), 0.99-0.79 (m, 6H)

Step 5:4-methoxy-N-[(1S)-3-methyl-1-[[(E,1S)-3-methylsulfonyl-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]allyl]carbamoyl]butyl]-1H-indole-2-carboxamide

To a mixture of 1-[ethoxy(methylsulfonylmethyl)phosphoryl]oxyethane(130.06 mg, 564.96 umol, 5 eq) in THF (2 mL) was added n-BuLi (2.5 M,180.79 uL, 4 eq) at 0° C. under N₂. The mixture was stirred at −75° C.for 30 min, then addedN-[(1S)-1-[[(1S)-1-formyl-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide (50 mg,112.99 umol, 1 eq). The mixture was stirred at −75° C. for 2 h. Once thereaction was completed, the reaction mixture was quenched by additionH₂O (10 mL) at 0° C., and then concentrated under reduced pressure togive a residue. The residue was purified by prep-HPLC to get thecompound4-methoxy-N-[(1S)-3-methyl-1-[[(E,1S)-3-methylsulfonyl-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]allyl]carbamoyl]butyl]-1H-indole-2-carboxamide(15 mg, 28.82 umol, 25.50% yield, 99.638% purity) as a solid. (ESI) m/z519.1 [M+H]⁺ column: Phenomenex luna C18 80*40 mm*3 um; mobile phase:[water (0.04% HCl)-ACN]; B %: 26%-52%, 7 min

¹H NMR (400 MHz, METHANOL-d₄) δ=7.33-7.26 (m, 1H), 7.20-7.10 (m, 1H),7.03 (d, J=8.3 Hz, 1H), 6.85 (dd, J=4.8, 15.3 Hz, 1H), 6.68 (dd, J=1.6,15.3 Hz, 1H), 6.52 (d, J=7.7 Hz, 1H), 4.77-4.67 (m, 1H), 4.61-4.50 (m,1H), 3.99-3.83 (m, 3H), 3.28-3.18 (m, 2H), 3.01-2.88 (m, 3H), 2.65-2.50(m, 1H), 2.39-2.22 (m, 1H), 2.15-1.97 (m, 1H), 1.91-1.62 (m, 5H),1.09-0.92 (m, 6H)

Example 10. Synthesis of Viral Protease Inhibitor Compound 740 and 741

Step 1: tert-butyl((S)-4-chloro-3-oxo-1-((S)-2-oxopyrrolidin-3-yl)butan-2-yl)carbamate

To a solution of methyl(2S)-2-(tert-butoxycarbonylamino)-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(0.6 g, 2.10 mmol, 1 eq) in THF (24 mL) was added chloro(iodo)methane(1.48 g, 8.38 mmol, 608.42 uL, 4 eq), then the solution was cooled to−70° C. and LDA (2 M, 6.29 mL, 6 eq) was added drop-wise. The reactionwas stirred at −70° C. for 1 h. Upon completion, the reaction mixturewas quenched by addition a mixture of AcOH (4.5 mL) and THF (22 mL) at−70° C., and then diluted with ethyl acetate (50 mL) and extracted withwater (30 mL*2), sat. NaHCO₃ (30 mL). The organic layers were washeddried over Na₂SO₄, filtered and concentrated under reduced pressure togive a residue. The residue was purified by column chromatography (SiO₂,petroleum ether:EtOAc=2:1 to 0:1) and then triturated with methyltertiary butyl ether:petroleum ether=4:1 (3 mL) to give tert-butylN-[(1S)-3-chloro-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]propyl]carbamate(0.35 g, 1.03 mmol, 49.32% yield, 90% purity) as a solid. MS (ESI) m/z308.0 [M+H]⁺.

¹H NMR (400 MHz, DMSO-d₆) δ=7.66 (br s, 1H), 7.53 (br d, J=7.7 Hz, 1H),4.61 (d, J=2.2 Hz, 2H), 4.22-4.10 (m, 1H), 3.21-3.11 (m, 2H), 2.34-2.06(m, 2H), 1.93-1.80 (m, 1H), 1.73-1.54 (m, 2H), 1.39 (s, 9H).

Step 2: (S)-3-((S)-2-amino-4-chloro-3-oxobutyl)pyrrolidin-2-one

A solution of tert-butylN-[(1S)-3-chloro-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]propyl]carbamate(0.33 g, 1.08 mmol, 1 eq) in HCl/EtOAc (4 M, 5 mL, 18.47 eq) was stirredat 0° C. for 1 h. Upon completion, the reaction mixture was concentratedunder reduced pressure to give(3S)-3-[(2S)-2-amino-4-chloro-3-oxo-butyl]pyrrolidin-2-one (0.3 g,crude, HCl) as an oil. MS (ESI) m/z 205.0 [M+H]⁺.

¹H NMR (400 MHz, DMSO-d₆) δ=8.75 (br s, 3H), 7.97 (br s, 1H), 4.96-4.91(m, 1H), 4.77 (s, 1H), 4.37-4.23 (m, 1H), 3.26-3.07 (m, 2H), 2.60 (br d,J=8.6 Hz, 1H), 2.37-2.27 (m, 1H), 1.96-1.90 (m, 1H), 1.79-1.66 (m, 1H).

Step 3:N—((S)-1-(((S)-4-chloro-3-oxo-1-((S)-2-oxopyrrolidin-3-yl)butan-2-yl)amino)-4-methyl-1-oxopentan-2-yl)-4-methoxy-1H-indole-2-carboxamide

A solution of(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4-methyl-pentanoic acid(416.53 mg, 1.37 mmol, 1.1 eq) in DMF (5 mL) was added HATU (946.18 mg,2.49 mmol, 2 eq) and NMM (251.71 mg, 2.49 mmol, 273.59 uL, 2 eq), thesolution was stirred at 0° C. for 0.5 h. Then a solution of(3S)-3-[(2S)-2-amino-4-chloro-3-oxo-butyl]pyrrolidin-2-one (0.3 g, 1.24mmol, 1 eq, HCl) in DMF (5 mL) was added drop-wise at 0° C. The reactionwas stirred at 25° C. for 0.5 h. Upon completion, the reaction mixturewas diluted with water (50 mL) at 0° C. drop-wise and extracted withEtOAc (20 mL*3). The combined organic layers were dried over Na₂SO₄,filtered and concentrated under reduced pressure to give a residue. Theresidue was purified by column chromatography (SiO₂, petroleumether:EtOAc=2:1 to 0:1). To giveN-[(1S)-1-[[(1S)-3-chloro-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]propyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide(0.3 g, 549.92 umol, 44.20% yield, 90% purity) as a solid. MS (ESI) m/z491.1 [M+H]⁺.

¹H NMR (400 MHz, DMSO-d₆) δ=11.58 (br s, 1H), 8.74-8.57 (m, 1H), 8.44(br d, J=5.0 Hz, 1H), 7.65 (br d, J=4.5 Hz, 1H), 7.37 (br s, 1H),7.15-7.06 (m, 1H), 7.01 (br d, J=8.1 Hz, 1H), 6.50 (br d, J=7.6 Hz, 1H),4.75-4.60 (m, 1H), 4.59-4.55 (m, 1H), 4.44 (br d, J=9.2 Hz, 2H), 3.88(s, 3H), 3.13-3.01 (m, 2H), 2.34-2.18 (m, 1H), 2.09 (br dd, J=2.5, 3.9Hz, 1H), 1.99-1.90 (m, 1H), 1.78-1.49 (m, 5H), 0.97-0.81 (m, 6H).

Step 4:(S)-3-((S)-2-(4-methoxy-1H-indole-2-carboxamido)-4-methylpentanamido)-2-oxo-4-((S)-2-oxopyrrolidin-3-yl)butyl2-oxo-2-phenylacetate

To a solution ofN-[(1S)-1-[[(1S)-3-chloro-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]propyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide(0.25 g, 509.19 umol, 1 eq) in DMF (6 mL) was added benzoylformic acid(99.38 mg, 661.94 umol, 1.3 eq) and CsF (177.89 mg, 1.17 mmol, 43.18 uL,2.3 eq). The reaction was stirred at 65° C. for 4 h under N₂ atmosphere.Upon completion, the reaction mixture was diluted with water (20 mL) andextracted with EtOAc (10 mL*3). The combined organic layers were driedover Na₂SO₄, filtered and concentrated under reduced pressure to give[(3S)-3-[[(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4-methyl-pentanoyl]amino]-2-oxo-4-[(3S)-2-oxopyrrolidin-3-yl]butyl]2-oxo-2-phenyl-acetate(0.3 g, crude) as an oil. MS (ESI) m/z 605.2 [M+H]⁺.

Step 5&6:N-[(1R)-1-[[(S)-3-hydroxy-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]propyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamideN-[(1S)-1-[[(1S)-3-hydroxy-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]propyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide

To a solution of[(3S)-3-[[(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4-methyl-pentanoyl]amino]-2-oxo-4-[(3S)-2-oxopyrrolidin-3-yl]butyl]2-oxo-2-phenyl-acetate (0.3 g, 496.16 umol, 1 eq) in MeOH (10 mL) wasadded K₂CO₃ (3.43 mg, 24.81 umol, 0.05 eq). The reaction was stirred at25° C. for 1 h. Upon completion, the reaction mixture was concentratedunder reduced pressure to give a residue. The residue was purified byprep-TLC (SiO₂, DCM:MeOH=10:1) to give the product.

¹H NMR (400 MHz, DMSO-d₆) δ=11.58 (s, 1H), 8.50 (d, J=7.8 Hz, 1H), 8.41(d, J=7.9 Hz, 1H), 7.63 (s, 1H), 7.35 (d, J=1.5 Hz, 1H), 7.14-7.05 (m,1H), 7.04-6.94 (m, 1H), 6.50 (d, J=7.7 Hz, 1H), 5.05-4.98 (m, 1H),4.57-4.46 (m, 1H), 4.41 (ddd, J=4.0, 7.7, 11.2 Hz, 1H), 4.34-4.25 (m,1H), 4.22-4.13 (m, 1H), 3.88 (s, 3H), 3.18-3.01 (m, 2H), 2.25-2.14 (m,1H), 2.13-2.04 (m, 1H), 1.99-1.84 (m, 1H), 1.77-1.48 (m, 5H), 0.93 (brd, J=6.2 Hz, 3H), 0.89 (br d, J=6.4 Hz, 3H).

To giveN-[(1S)-1-[[(1S)-3-hydroxy-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]propyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide(23.86 mg, 49.08 umol, 9.89% yield, 97.2% purity) as a solid. MS (ESI)m/z 473.2 [M+H]⁺. The product was separated by chiral-SFC (column:DAICEL CHIRALCEL OJ (250 mm*30 mm, 10 um); mobile phase: [Neu-MeOH]; B%: 20%-20%, 15 min) to giveN-[(1R)-1-[[(1S)-3-hydroxy-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]propyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide(15.43 mg, 31.22 umol, 6.29% yield, 95.6% purity) as a solid. MS (ESI)m/z 473.2 [M+H]⁺.

¹H NMR (400 MHz, DMSO-d₆) δ=11.57 (s, 1H), 8.45 (br d, J=8.1 Hz, 1H),8.41 (br d, J=7.8 Hz, 1H), 7.62 (s, 1H), 7.36 (d, J=1.3 Hz, 1H),7.14-7.05 (m, 1H), 7.04-6.97 (m, 1H), 6.50 (d, J=7.6 Hz, 1H), 5.06 (brs, 1H), 4.62-4.38 (m, 2H), 4.30-4.19 (m, 1H), 4.19-4.09 (m, 1H), 3.88(s, 3H), 3.19-3.01 (m, 2H), 2.37-2.22 (m, 1H), 2.09 (br dd, J=3.2, 6.2Hz, 1H), 1.99-1.86 (m, 1H), 1.80-1.43 (m, 5H), 0.94 (d, J=6.2 Hz, 3H),0.89 (d, J=6.2 Hz, 3H).

Example 11. Synthesis of Viral Protease Inhibitor Compound 143

Step 1: methyl(2S)-2-[[(2S)-2-amino-4-methyl-pentanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate

A mixture of methyl(2S)-2-[[(2S)-2-(tert-butoxycarbonylamino)-4-methyl-pentanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(250 mg, 625.81 umol, 1 eq) was added HCl/EtOAc (8 mL) at 25° C. for 1h. Upon completion, the reaction mixture was concentrated under reducedpressure to give a residue get a product methyl(2S)-2-[[(2S)-2-amino-4-methyl-pentanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(230 mg, crude) as an oil. MS (ESI) W/z 300.0 [M+H]⁺.

Step 2: methyl(2S)-2-[[(2S)-4-methyl-2-[[(E)-3-phenylprop-2-enoyl]amino]pentanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate

A mixture of methyl(2S)-2-[[(2S)-2-amino-4-methyl-pentanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(230 mg, 684.88 umol, 1 eq, HCl) and (E)-3-phenylprop-2-enoic acid(202.94 mg, 1.37 mmol, 162.35 uL, 2 eq) in DMF (2 mL) and DCM (4 mL),and added EDCI (262.59 mg, 1.37 mmol, 2 eq) and DMAP (167.34 mg, 1.37mmol, 2 eq). The mixture was stirred at 25° C. for 1 h. Upon completion,the reaction mixture was diluted with H₂O (10 mL) and extracted with DCM(10 mL*3). The combined organic layers were washed with brine (50 mL),dried over Na₂SO₄, filtered and concentrated under reduced pressure togive a residue. The residue was purified by silica gel chromatography(SiO₂, petroleum ether:EtOAc=1:1) to get a product methyl(2S)-2-[[(2S)-4-methyl-2-[[(E)-3-phenylprop-2-enoyl]amino]pentanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(200 mg, 465.65 umol, 67.99% yield) as an oil. MS (ESI) m/z 430.1[M+H]⁺.

Step 3:(2S)—N-[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]-4-methyl-2-[[(E)-3-phenylprop-2-enoyl]amino]pentanamide

A mixture of methyl(2S)-2-[[(2S)-4-methyl-2-[[(E)-3-phenylprop-2-enoyl]amino]pentanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(200 mg, 465.65 umol, 1 eq) in NH₃/MeOH (7 M, 7 mL, 97% purity, 105.23eq) heated to 80° C. for 16 h in the sealed tube. Upon completion, thereaction mixture was concentrated under reduced pressure to give aresidue to get the product(2S)—N-[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]-4-methyl-2-[[(E)-3-phenylprop-2-enoyl]amino]pentanamide(200 mg, crude) as an oil. MS (ESI) m/z 415.1 [M+H]⁺.

Step 4:(2S)—N-[(1S)-1-cyano-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]-4-methyl-2-[[(E)-3-phenylprop-2-enoyl]amino]pentanamide

A mixture of(2S)—N-[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]-4-methyl-2-[[(E)-3-phenylprop-2-enoyl]amino]pentanamide(200 mg, 482.51 umol, 1 eq) in DCM (2 mL) was addedmethoxycarbonyl-(triethylammonio)sulfonyl-azanide (574.93 mg, 2.41 mmol,5 eq), the mixture was stirred at 25° C. for 1 h. Upon completion, thereaction mixture was concentrated under reduced pressure to give aresidue. The residue was purified by prep-HPLC (column: Waters XbridgePrep OBD C18 150*40 mm*10 um; mobile phase: [water (10 mM NH₄HCO₃)-ACN];B %: 25%-55%, 8 min) to give a product(2S)—N-[(1S)-1-cyano-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]-4-methyl-2-[[(E)-3-phenylprop-2-enoyl]amino]pentanamide(23.1 mg, 58.26 umol, 12.07% yield, 100% purity) as a solid. MS (ESI)m/z 397.2 [M+H]⁺.

¹H NMR (400 MHz, CDCl₃)=8.70 (br d, J=6.6 Hz, 1H), 7.66-7.55 (m, 1H),7.54-7.44 (m, 2H), 7.35 (br s, 3H), 6.72-6.52 (m, 2H), 6.47 (d, J=15.7Hz, 1H), 5.02-4.67 (m, 2H), 3.49-3.22 (m, 2H), 2.56-2.27 (m, 3H),2.02-1.88 (m, 1H), 1.88-1.80 (m, 1H), 1.75-1.61 (m, 3H), 1.07-0.87 (m,6H)

Example 12. Synthesis of Viral Protease Inhibitor Compound 598

Step 1: methyl(2S)-2-[[(2S)-2-amino-4-methyl-pentanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate

A mixture of methyl(2S)-2-[[(2S)-2-(tert-butoxycarbonylamino)-4-methyl-pentanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(300 mg, 750.98 umol, 1 eq) was added HCl/EtOAc (4 M, 6 mL, 31.96 eq) at25° C. for 1 h. Upon completion, the product blow-dried directly with N₂to get the product methyl(2S)-2-[[(2S)-2-amino-4-methyl-pentanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(260 mg, crude) as an oil. MS (ESI) m/z 300.1 [M+H]⁺.

Step 2: methyl(2S)-2-[[(2S)-2-[[(E)-3-(4-chloro-2-fluoro-phenyl)prop-2-enoyl]amino]-4-methyl-pentanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate

A mixture of methyl(2S)-2-[[(2S)-2-amino-4-methyl-pentanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(250 mg, 744.43 umol, 1 eq, HCl) and(E)-3-(4-chloro-2-fluoro-phenyl)prop-2-enoic acid (298.66 mg, 1.49 mmol,81.96 uL, 2 eq) in DMF (2 mL) and DCM (4 mL) was added EDCI (285.42 mg,1.49 mmol, 2 eq) and DMAP (181.89 mg, 1.49 mmol, 2 eq). The mixture wasstirred at 25° C. for 1 h. Upon completion, the reaction mixture wasdiluted with H₂O (10 mL) and extracted with DCM (10 mL*3). The combinedorganic layers were washed with brine (50 mL), dried over Na₂SO₄,filtered and concentrated under reduced pressure to give a residue. Theresidue was purified by silica gel chromatography (SiO₂, petroleumether:EtOAc=0:1) to get a product methyl(2S)-2-[[(2S)-2-[[(E)-3-(4-chloro-2-fluoro-phenyl)prop-2-enoyl]amino]-4-methyl-pentanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(80 mg, 165.99 umol, 22.30% yield) as an oil. MS (ESI) m/z 482.1 [M+H]⁺.

Step 3:(2S)—N-[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]-2-[[(E)-3-(4-chloro-2-fluoro-phenyl)prop-2-enoyl]amino]-4-methyl-pentanamide

A mixture of methyl(2S)-2-[[(2S)-2-[[(E)-3-(4-chloro-2-fluoro-phenyl)prop-2-enoyl]amino]-4-methyl-pentanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(70 mg, 145.25 umol, 1 eq) in NH₃/MeOH (7 M, 6 mL, 97% purity, 289.17eq) was stirred at 80° C. for 16 h. Upon completion, the reactionmixture was concentrated under reduced pressure to give the product(2S)—N-[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]-2-[[(E)-3-(4-chloro-2-fluoro-phenyl)prop-2-enoyl]amino]-4-methyl-pentanamide(70 mg, crude) as an oil. MS (ESI) m/z 467.1 [M+H]⁺.

Step 4:(2S)-2-[[(E)-3-(4-chloro-2-fluoro-phenyl)prop-2-enoyl]amino]-N-[(1S)-1-cyano-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]-4-methyl-pentanamide

A mixture of(2S)—N-[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]-2-[[(E)-3-(4-chloro-2-fluoro-phenyl)prop-2-enoyl]amino]-4-methyl-pentanamide(70 mg, 149.91 umol, 1 eq) in DCM (1.5 mL) was addedmethoxycarbonyl-(triethylammonio)sulfonyl-azanide (160.77 mg, 674.62umol, 4.5 eq), the mixture was stirred at 25° C. for 1 h. Uponcompletion, the reaction mixture was concentrated under reduced pressureto give a residue. The residue was purified by prep-HPLC (column: WatersXbridge Prep OBD C18 150*40 mm*10 um; mobile phase: [water (10 mMNH₄HCO₃)-ACN]; B %: 30%-60%, 8 min) to get product(2S)—N-[(1S)-1-cyano-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]-4-methyl-2-[[(E)-3-phenylprop-2-enoyl]amino]pentanamide(13.4 mg, 58.26 umol, 12.07% yield, 100% purity) as a solid. MS (ESI)m/z 449.1 [M+H]⁺.

¹H NMR (400 MHz, CDCl₃) δ=8.67 (br d, J=5.7 Hz, 1H), 7.63 (d, J=15.7 Hz,1H), 7.42 (t, J=8.3 Hz, 1H), 7.19-7.06 (m, 2H), 6.55 (d, J=15.7 Hz, 1H),6.34 (br s, 1H), 6.19 (br s, 1H), 4.83-4.67 (m, 2H), 3.47-3.33 (m, 2H),2.58-2.28 (m, 3H), 2.04 (br s, 1H), 1.95-1.82 (m, 1H), 1.81-1.62 (m,3H), 0.99 (d, J=6.0 Hz, 6H)

Example 13. Synthesis of Viral Protease Inhibitor Compound 149

Step 1: methyl (2S)-2-amino-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate

To a mixture of methyl(2S)-2-(tert-butoxycarbonylamino)-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(500 mg, 1.75 mmol, 1 eq) in HCl/EtOAc (4 M, 20 mL). The mixture wasstirred at 25° C. and stirred for 1 h. Once the reaction was completed,the reaction was concentrated to give the crude methyl(2S)-2-amino-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate (400 mg, crude)(oil). The crude product was used directly without further purification.MS (ESI) m/z 187.1 [M+H]⁺

Step 2: methyl(2S)-2-[[(2S)-2-(tert-butoxycarbonylamino)-2-indan-2-yl-acetyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate

To a mixture of methyl(2S)-2-amino-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate (190 mg, 1.02 mmol,1 eq) and (2S)-2-(tert-butoxycarbonylamino)-2-indan-2-yl-acetic acid(297.27 mg, 1.02 mmol, 1 eq) in DCM (9 mL) and DMF (3 mL) was added DMAP(249.31 mg, 2.04 mmol, 2 eq) and EDCI (391.21 mg, 2.04 mmol, 2 eq). Themixture was stirred at 25° C. for 2 h. Once the reaction was completed,the reaction was poured into ice-water (30 mL) and extracted with EtOAc(20 mL*3). The combined organic phase was dried with anhydrous Na₂SO₄,filtered and concentrated in vacuum. The residue was purified by silicagel chromatography (column height: 250 mm, diameter: 100 mm, 100-200mesh silica gel, petroleum ether/EtOAc=1/1, 0/1) to give methyl(2S)-2-[[(2S)-2-(tert-butoxycarbonylamino)-2-indan-2-yl-acetyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(300 mg, 522.27 umol, 51.18% yield, 80% purity) (solid). MS (ESI) m/z460.3 [M+H]⁺

Step 3: methyl(2S)-2-[[(2S)-2-(tert-butoxycarbonylamino)-2-indan-2-yl-acetyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate

To a mixture of (S)-methyl2-((tert-butoxycarbonyl)amino)-3-((S)-2-oxopyrrolidin-3-yl)propanoate(400 mg, 870.4 umol, 1 eq) in HCl/EtOAc (4 M, 20 mL). The mixture wasstirred at 25° C. for 2 h. Once the reaction was completed, the reactionmixture was concentrated to get the product methyl(2S)-2-[[(2S)-2-(tert-butoxycarbonylamino)-2-indan-2-yl-acetyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(330 mg, crude) was obtained as an oil and used directly next step. MS(ESI) m/z 360.2 [M+H]⁺

Step 4: methyl(2S)-2-[[(2S)-2-amino-2-indan-2-yl-acetyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate

To a mixture of methyl(2S)-2-[[(2S)-2-(tert-butoxycarbonylamino)-2-indan-2-yl-acetyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(300 mg, 652.84 umol, 1 eq) and 4-methoxy-1H-indole-2-carboxylic acid(149.77 mg, 783.40 umol, 1.2 eq) in DCM (6 mL) and DMF (2 mL) was addedDMAP (159.51 mg, 1.31 mmol, 2 eq) and EDCI (250.30 mg, 1.31 mmol, 2 eq).The mixture was stirred at 25° C. and stirred for 2 h. Once the reactionwas completed, the reaction was poured into ice-water (30 mL) andextracted with ethyl acetate (20 mL*3). The combined organic phase wasdried with anhydrous Na₂SO₄, filtered and concentrated in vacuum. Theresidue was purified by silica gel chromatography (column height: 250mm, diameter: 100 mm, 100-200 mesh silica gel, petroleum ether/ethylacetate=1/1, 0/1) to give methyl(2S)-2-[[(2S)-2-amino-2-indan-2-yl-acetyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(300 mg, 506.96 umol, 77.66% yield, 90% purity) (solid). MS (ESI) m/z533.2 [M+H]⁺

Step 5:N-[(1S)-1-[[(1S)-2-amino-1-[(3-methylimidazol-4-yl)methyl]-2-oxo-ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide

To a mixture of (S)-methyl2-((S)-2-(2,3-dihydro-1H-inden-2-yl)-2-(4-methoxy-1H-indole-2-carboxamido)acetamido)-3-((S)-2-oxopyrrolidin-3-yl)propanoate(100 mg, 187.76 umol, 1 eq) was added ammonia (3.20 mg, 187.76 umol,3.13 uL, 1 eq). The mixture was stirred at 80° C. and stirred for 16 h.Once the reaction was completed, the reaction was concentrated to givethe crudeN—((S)-2-(((S)-1-amino-1-oxo-3-((S)-2-oxopyrrolidin-3-yl)propan-2-yl)amino)-1-(2,3-dihydro-1H-inden-2-yl)-2-oxoethyl)-4-methoxy-1H-indole-2-carboxamide(70 mg, 108.20 umol, 57.62% yield, 80% purity) as a solid. Crude productwas used directly without further purification. MS (ESI) m/z 518.2[M+H]⁺

Step 6:N-[(1S)-2-[[(1S)-1-cyano-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]amino]-1-indan-2-yl-2-oxo-ethyl]-4-methoxy-1H-indole-2-carboxamide

To a mixture ofN-[(1S)-2-[[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]amino]-1-indan-2-yl-2-oxo-ethyl]-4-methoxy-1H-indole-2-carboxamide(60 mg, 115.93 umol, 1 eq) andmethoxycarbonyl-(triethylammonio)sulfonyl-azanide (55.25 mg, 231.85umol, 2 eq) in DCM (0.5 mL). The mixture was stirred at 25° C. andstirred for 2 h. Once the reaction was completed, the reaction waspoured into ice-water (30 mL) and extracted with DCM (20 mL*3). Thecombined organic phase was dried with anhydrous Na₂SO₄, filtered andconcentrated in vacuum. The residue was purified by prep-HPLC (column:Phenomenex Gemini-NX 80*40 mm*3 um; mobile phase: [water (10 MmNH₄HCO₃)-ACN]; B %: 20%-50%, 8 min) to giveN-[(1S)-2-[[(1S)-1-cyano-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]amino]-1-indan-2-yl-2-oxo-ethyl]-4-methoxy-1H-indole-2-carboxamide(23.83 mg, 47.70 umol, 41.15% yield, 100% purity) (solid). MS (ESI) m/z500.3 [M+H]⁺.

¹H NMR (400 MHz, METHANOL-d₄) δ ppm 7.26 (s, 1H), 7.13-7.17 (m, 2H),7.11-7.12 (m, 3H), 7.03 (s, 1H), 6.55-6.52 (d, J=12.4 Hz, 1H), 5.05-5.01(m, 1H), 4.85-5.00 (m, 1H), 3.92 (s, 3H), 3.25-3.26 (m, 3H), 3.21-3.24(m, 2H), 2.90-3.01 (m, 2H), 2.88-2.89 (m, 1H), 2.31-3.33 (m, 2H),1.81-1.92 (m, 2H)

Example 14. Synthesis of Viral Protease Inhibitor Compound 165

Step 1: methyl (2S)-2-amino-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate;hydrochloride

Methyl(2S)-2-(tert-butoxycarbonylamino)-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(250 mg, 873.14 umol, 1 eq) was added HCl/EtOAc (4 M, 30 mL) at 25° C.The mixture was stirred at 25° C. for 1 h. The reaction mixture wasconcentrated under reduced pressure to give a product methyl(2S)-2-amino-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate; hydrochloride (200mg, crude) as a solid and used directly for next step.

Step 2:(2S,4R)-(9H-fluoren-9-yl)methyl-4-(tert-butoxy)-2-(((S)-1-methoxy-1-oxo-3-((S)-2-oxopyrrolidin-3-yl)propan-2-yl)carbamoyl)pyrrolidine-1-carboxylate

A mixture of methyl (2S)-2-amino-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(190 mg, 853.29 umol, 1 eq, HCl),(2S,4R)-4-tert-butoxy-1-(9H-fluoren-9-ylmethoxycarbonyl)pyrrolidine-2-carboxylicacid (349.40 mg, 853.29 umol, 1 eq), EDCI (327.15 mg, 1.71 mmol, 2 eq),DMAP (208.49 mg, 1.71 mmol, 2 eq), DMF (3 mL) and DCM (6 mL) was stirredat 25° C. for 1 h. The reaction mixture was diluted with H₂O (30 mL) andextracted with DCM (30 mL*3). The combined organic layers were washedwith brine (50 mL), dried over Na₂SO₄, filtered and concentrated underreduced pressure to give a residue. The residue was purified by columnchromatography (SiO₂, petroleum ether/EtOAc=0/1) to get the product(2S,4R)-(9H-fluoren-9-yl)methyl-4-(tert-butoxy)-2-(((S)-1-methoxy-1-oxo-3-((S)-2-oxopyrrolidin-3-yl)propan-2-yl)carbamoyl)pyrrolidine-1-carboxylate(230 mg, 319.96 umol, 37.50% yield, 80.36% purity), as an oil. MS (ESI)m/z 578.2 [M+H]⁺

Step 3:(S)-methyl-2-((2S,4R)-4-(tert-butoxy)pyrrolidine-2-carboxamido)-3-((S)-2-oxopyrrolidin-3-yl)propanoate

A mixture of(2S,4R)-(9H-fluoren-9-yl)methyl-4-(tert-butoxy)-2-(((S)-1-methoxy-1-oxo-3-((S)-2-oxopyrrolidin-3-yl)propan-2-yl)carbamoyl)pyrrolidine-1-carboxylate(170 mg, 294.29 umol, 1 eq), piperidine (3.76 g, 8.83 mmol, 4.36 mL, 20%purity, 30 eq), DMF (1 mL) was stirred at 25° C. for 1 h. The reactionmixture was concentrated under reduced pressure to give a residue. Theresidue was purified by prep-TLC (DCM/MeOH=10/1) to get the product(S)-methyl-2-((2S,4R)-4-(tert-butoxy)pyrrolidine-2-carboxamido)-3-((S)-2-oxopyrrolidin-3-yl)propanoate(40 mg, 112.54 umol, 38.24% yield) as an oil.

Step 4:(S)-methyl-2-((2S,4R)-4-(tert-butoxy)-1-(4-methoxy-1H-indole-2-carbonyl)pyrrolidine-2-carboxamido)-3-((S)-2-oxopyrrolidin-3-yl)propanoate

A mixture of(S)-methyl-2-((2S,4R)-4-(tert-butoxy)pyrrolidine-2-carboxamido)-3-((S)-2-oxopyrrolidin-3-yl)propanoate(40 mg, 112.54 umol, 1 eq), 4-methoxy-1H-indole-2-carboxylic acid (21.52mg, 112.54 umol, 1 eq), EDCI (43.15 mg, 225.08 umol, 2 eq), DMAP (27.50mg, 225.08 umol, 2 eq), DMF (0.5 mL) and DCM (1 mL) was stirred at 25°C. for 1 h. The reaction mixture was diluted with H₂O (30 mL) andextracted with DCM (30 mL*3). The combined organic layers were washedwith brine (50 mL), dried over Na₂SO₄, filtered and concentrated underreduced pressure to give a residue. The residue was purified by columnchromatography (SiO₂, petroleum ether/EtOAc=0/1) to get the compound(S)-methyl-2-((2S,4R)-4-(tert-butoxy)-1-(4-methoxy-1H-indole-2-carbonyl)pyrrolidine-2-carboxamido)-3-((S)-2-oxopyrrolidin-3-yl)propanoate(30 mg, 22.33 umol, 19.84% yield), as an oil.

Step 5:(2S,4R)-N—((S)-1-amino-1-oxo-3-((S)-2-oxopyrrolidin-3-yl)propan-2-yl)-4-(tert-butoxy)-1-(4-methoxy-1H-indole-2-carbonyl)pyrrolidine-2-carboxamide

A mixture of(S)-methyl-2-((2S,4R)-4-(tert-butoxy)-1-(4-methoxy-1H-indole-2-carbonyl)pyrrolidine-2-carboxamido)-3-((S)-2-oxopyrrolidin-3-yl)propanoate(27 mg, 20.10 umol, 39.35% purity, 1 eq) and NH₃/MeOH (7 M, 3 mL) wasstirred at 80° C. for 16 h. The reaction mixture was concentrated underreduced pressure to give a product(2S,4R)-N—((S)-1-amino-1-oxo-3-((S)-2-oxopyrrolidin-3-yl)propan-2-yl)-4-(tert-butoxy)-1-(4-methoxy-1H-indole-2-carbonyl)pyrrolidine-2-carboxamide(22 mg, crude) as a solid. MS (ESI) m/z 514.2 [M+H]⁺

Step 6:(2S,4R)-4-(tert-butoxy)-N—((S)-1-cyano-2-((S)-2-oxopyrrolidin-3-yl)ethyl)-1-(4-methoxy-1H-indole-2-carbonyl)pyrrolidine-2-carboxamide

A mixture of(2S,4R)-N—((S)-1-amino-1-oxo-3-((S)-2-oxopyrrolidin-3-yl)propan-2-yl)-4-(tert-butoxy)-1-(4-methoxy-1H-indole-2-carbonyl)pyrrolidine-2-carboxamide(20 mg, 38.94 umol, 1 eq), Burgess reagent (27.84 mg, 116.83 umol, 3 eq)and DCM (1 mL) was stirred at 25° C. for 4 h. The reaction mixture wasconcentrated under reduced pressure to give a residue. The residue waspurified by prep-HPLC (column: Phenomenex Gemini-NX C18 75*30 mm*3 um;mobile phase: [water (0.05% NH₃H₂O+10 mM NH₄HCO₃)-ACN]; B %: 20%-40%, 8min) to get the product(2S,4R)-4-(tert-butoxy)-N—((S)-1-cyano-2-((S)-2-oxopyrrolidin-3-yl)ethyl)-1-(4-methoxy-1H-indole-2-carbonyl)pyrrolidine-2-carboxamide(5 mg, 10.09 umol, 25.91% yield, 100% purity), as a solid. MS (ESI) m/z496.3 [M+H]⁺.

¹H NMR (400 MHz, DMSO-d₆) δ=11.73-11.43 (m, 1H), 9.26-8.84 (m, 1H),7.84-7.49 (m, 1H), 7.19-7.07 (m, 1H), 7.05-6.96 (m, 1H), 6.94-6.65 (m,1H), 6.57-6.41 (m, 1H), 5.08-4.92 (m, 1H), 4.85-4.40 (m, 2H), 4.34-4.08(m, 1H), 3.98-3.75 (m, 3H), 3.74-3.50 (m, 1H), 3.22-2.80 (m, 2H),2.47-2.37 (m, 1H), 2.27-2.04 (m, 3H), 2.03-1.87 (m, 1H), 1.86-1.36 (m,2H), 1.15 (s, 9H)

Example 15. Synthesis of Viral Protease Inhibitor Compound 167

Step 1: (S)-methyl 2-amino-3-((S)-2-oxopyrrolidin-3-yl)propanoate

Methyl(2S)-2-(tert-butoxycarbonylamino)-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(300 mg, 1.05 mmol, 1 eq) in HCl/EtOAc (4 M, 5 mL, 19.09 eq) was stirredat 25° C. for 1 h. Upon completion, the mixture was concentrated underthe reduced pressure affording the product methyl(2S)-2-amino-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate (HCl salt, 210 mg,crude) as a solid.

Step 2:(2S,4S)-(9H-fluoren-9-yl)methyl4-cyclohexyl-2-(((S)-1-methoxy-)-oxo-3-((S)-2-oxopyrrolidin-3-yl)propan-2-yl)carbamoyl)pyrrolidine-1-carboxylate

Methyl (2S)-2-amino-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate (200 mg,1.07 mmol, 1 eq) and(2S,4S)-4-cyclohexyl-1-(9Hfluoren-9-ylmethoxycarbonyl)pyrrolidine-2-carboxylicacid (450.58 mg, 1.07 mmol, 1 eq) in DMF (1 mL) and DCM (2 mL) was addedDMAP (262.43 mg, 2.15 mmol, 2 eq) and EDCI (411.80 mg, 2.15 mmol, 2 eq).The mixture was stirred at 25° C. for 4 h. Upon completion, the reactionmixture was quenched by addition H₂O (10 mL), and then extracted withEtOAc (10 mL*3). The combined organic layers were washed with brine (10mL), dried over Na₂SO₄, filtered and concentrated under reduced pressureto give a residue. The residue was purified by column chromatography(SiO₂, petroleum ether:EtOAc=5:1 to 1:1) affording the product9H-fluoren-9-ylmethyl(2S,4S)-4-cyclohexyl-2-[[(1S)-2-methoxy-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]carbamoyl]pyrrolidine-1-carboxylate(500 mg, 850.77 umol, 79.21% yield) as a solid. MS (ESI) m/z 588.3[M+H]⁺

Step 3:(S)-methyl2-((2S,4S)-4-cyclohexylpyrrolidine-2-carboxamido)-3-((S)-2-oxopyrrolidin-3-yl)propanoate

9H-fluoren-9-ylmethyl(2S,4S)-4-cyclohexyl-2-[[(1S)-2-methoxy-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]carbamoyl]pyrrolidine-1-carboxylate(480 mg, 816.74 umol, 1 eq) in DMF (4 mL) and PIPERIDINE (862.20 mg,10.13 mmol, 1 mL, 12.40 eq) was stirred at 25° C. for 0.5 h. Uponcompletion, the mixture was drying with N₂ and then diluted with DCM (10mL), concentrated under the reduced pressure to give a residue. Theresidue was purified by prep-TLC (SiO₂, DCM:MeOH=10:1) affording theproduct methyl(2S)-2-[[(2S,4S)-4-cyclohexylpyrrolidine-2-carbonyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(210 mg, 574.61 umol, 70.35% yield) as a solid.

Step 4:(S)-methyl2-((2S,4S)-4-cyclohexyl-1-(4-methoxy-1H-indole-2-carbonyl)pyrrolidine-2-carboxamido)-3-((S)-2-oxopyrrolidin-3-yl)propanoate

Methyl(2S)-2-[[(2S,4S)-4-cyclohexylpyrrolidine-2-carbonyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(200 mg, 547.25 umol, 1 eq) and 4-methoxy-1H-indole-2-carboxylic acid(104.62 mg, 547.25 umol, 1 eq) in DMF (2 mL) and DCM (3 mL) was addedDMAP (133.71 mg, 1.09 mmol, 2 eq) and EDCI (209.82 mg, 1.09 mmol, 2 eq).The mixture was stirred at 25° C. for 4 h. Upon completion, the reactionmixture was quenched by addition H₂O (10 mL), and then extracted withDCM (10 mL*3). The combined organic layers were washed with brine (10mL), dried over Na₂SO₄, filtered and concentrated under reduced pressureto give a residue. The residue was purified by prep-TLC (SiO₂, petroleumether:EtOAc=0:1) affording the productmethyl(2S)-2-[[(2S,4S)-4-cyclohexyl-1-(4-methoxy-1H-indole-2-carbonyl)pyrrolidine-2-carbonyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(210 mg, 389.88 umol, 71.24% yield) as a solid. MS (ESI) m/z 539.2[M+H]⁺

Step 5:(2S,4S)-N—((S)-1-amino-1-oxo-3-((S)-2-oxopyrrolidin-3-yl)propan-2-yl)-4-cyclohexyl-1-(4-methoxy-1H-indole-2-carbonyl)pyrrolidine-2-carboxamide

Methyl(2S)-2-[[(2S,4S)-4-cyclohexyl-1-(4-methoxy-1H-indole-2-carbonyl)pyrrolidine-2-carbonyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(200 mg, 371.31 umol, 1 eq) was in NH₃/MeOH (7 M, 10 mL, 188.52 eq). Themixture was stirred at 80° C. for 16 h. Upon completion, the mixture wasconcentrated under the reduced pressure affording the product(2S,4S)—N-[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]-4-cyclohexyl-1-(4-methoxy-1Hindole-2-carbonyl)pyrrolidine-2-carboxamide(110 mg, crude) as a solid. MS (ESI) m/z 524.2 [M+H]⁺

Step 6:(2S,4S)-N—((S)-1-cyano-2-((S)-2-oxopyrrolidin-3-yl)ethyl)-4-cyclohexyl-1-(4-methoxy-1H-indole-2-carbonyl)pyrrolidine-2-carboxamide

(2S,4S)—N-[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]-4-cyclohexyl-1-(4-methoxy-1H-indole-2-carbonyl)pyrrolidine-2-carboxamide(100 mg, 190.98 umol, 1 eq) in DCM (1 mL) was addedmethoxycarbonyl-(triethylammonio)sulfonyl-azanide (227.55 mg, 954.89umol, 5 eq). The mixture was stirred at 25° C. for 3 h. Upon completion,the mixture was concentrated under the reduced pressure to give aresidue. The residue was purified by prep-HPLC (column: Waters XbridgeBEH C18 100*25 mm*5 um; mobile phase: [water (10 mM NH₄HCO₃)-ACN]; B %:30%-60%, 10 min) affording the product(2S,4S)—N-[(1S)-1-cyano-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]-4-cyclohexyl-1-(4-methoxy-1H-indole-2-carbonyl)pyrrolidine-2-carboxamide(30.7 mg, 60.17 umol, 31.51% yield, 99.1% purity) as a solid. MS (ESI)m/z 506.3 [M+H]⁺

¹H NMR (400 MHz, MeOD-d₄) δ=7.23-6.82 (m, 3H), 6.60-6.36 (m, 1H),5.21-4.96 (m, 1H), 4.72-4.56 (m, 1H), 4.34-4.07 (m, 1H), 4.00-3.80 (m,3H), 3.57 (br t, J=9.4 Hz, 1H), 3.02-2.54 (m, 1H), 2.46-0.92 (m, 20H)

Example 16. Synthesis of Viral Protease Inhibitor Compound 209

Step 1: (S)-methyl 2-amino-3-((S)-2-oxopyrrolidin-3-yl)propanoate

A mixture of methyl(2S)-2-(tert-butoxycarbonylamino)-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(0.55 g, 1.92 mmol, 1 eq) and HCl/EtOAc (4 M, 10 mL, 20.82 eq) wasstirred at 25° C. for 0.5 h. Upon completion, the reaction mixture wasconcentrated under reduced pressure to give (S)-methyl2-amino-3-((S)-2-oxopyrrolidin-3-yl)propanoate (0.35 g, crude) as anoil.

Step 2: (2S,4S)-tert-butyl2-(((S)-1-methoxy-1-oxo-3-((S)-2-oxopyrrolidin-3-yl)propan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate

A mixture of (S)-methyl 2-amino-3-((S)-2-oxopyrrolidin-3-yl)propanoate(0.15 g, 805.55 umol, 1 eq),(2S,4S)-1-tert-butoxycarbonyl-4-phenyl-pyrrolidine-2-carboxylic acid(234.69 mg, 805.55 umol, 1 eq), DMAP (196.83 mg, 1.61 mmol, 2 eq), EDCI(308.85 mg, 1.61 mmol, 2 eq) in DMF (1 mL) and DCM (2 mL) was stirred at25° C. for 0.5 h. Upon completion, the reaction mixture was diluted withwater (10 mL) and extracted with ethyl acetate (5 mL*3). The combinedorganic layers were dried over Na₂SO₄, filtered and concentrated underreduced pressure to give a residue. The residue was purified by columnchromatography (SiO₂, petroleum ether:EtOAc=2:1 to 0:1) to give(2S,4S)-tert-butyl2-[[(1S)-2-methoxy-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]carbamoyl]-4-phenyl-pyrrolidine-1-carboxylate(0.25 g, 500.51 umol, 62.13% yield, 92% purity) as a colorless oil. MS(ESI) m/z 460.1 [M+H]⁺.

Step 3: (S)-methyl3-((S)-2-oxopyrrolidin-3-yl)-2-((2S,4S)-4-phenylpyrrolidine-2-carboxamido)propanoate

A mixture of tert-butyl(2S,4S)-2-[[(1S)-2-methoxy-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]carbamoyl]-4-phenyl-pyrrolidine-1-carboxylate(0.25 g, 544.03 umol, 1 eq) and HCl/EtOAc (4 M, 10 mL, 73.53 eq) wasstirred at 25° C. for 0.5 h. Upon completion, the reaction mixture wasconcentrated under reduced pressure to give methyl(2S)-3-[(3S)-2-oxopyrrolidin-3-yl]-2-[[(2S,4S)-4-phenylpyrrolidine-2-carbonyl]amino]propanoate(0.2 g, crude) as an oil. MS (ESI) m/z 360.1 [M+H]⁺.

Step 4: (S)-methyl2-((2S,4S)-1-((E)-3-(4-chloro-2-fluorophenyl)acryloyl)-4-phenylpyrrolidine-2-carboxamido)-3-((S)-2-oxopyrrolidin-3-yl)propanoate

A mixture of methyl(2S)-3-[(3S)-2-oxopyrrolidin-3-yl]-2-[[(2S,4S)-4-phenylpyrrolidine-2-carbonyl]amino]propanoate(0.17 g, 472.99 umol, 1 eq),(E)-3-(4-chloro-2-fluoro-phenyl)prop-2-enoic acid (94.88 mg, 472.99umol, 1 eq), T3P (451.48 mg, 709.48 umol, 421.95 uL, 50% purity, 1.5eq), TEA (143.58 mg, 1.42 mmol, 197.50 uL, 3 eq) in DMF (4 mL) wasdegassed stirred at 25° C. for 0.5 h. Upon completion, the reactionmixture was diluted with water (20 mL) and extracted with ethyl acetate(10 mL*3). The combined organic layers were dried over Na₂SO₄, filteredand concentrated under reduced pressure to give a residue. The residuewas purified by column chromatography (SiO₂, petroleum ether:EtOAc=2:1to 0:1) to give methyl(2S)-2-[[(2S,4S)-1-[(E)-3-(4-chloro-2-fluoro-phenyl)prop-2-enoyl]-4-phenyl-pyrrolidine-2-carbonyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(0.11 g, 162.36 umol, 34.33% yield, 80% purity) as a solid. MS (ESI) m/z542.1 [M+H]⁺.

Step 5:(2S,4S)-N—((S)-1-amino-1-oxo-3-((S)-2-oxopyrrolidin-3-yl)propan-2-yl)-1-((E)-3-(4-chloro-2-fluorophenyl)acryloyl)-4-phenylpyrrolidine-2-carboxamide

A mixture of methyl(2S)-2-[[(2S,4S)-1-[(E)-3-(4-chloro-2-fluoro-phenyl)prop-2-enoyl]-4-phenyl-pyrrolidine-2-carbonyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(0.1 g, 184.50 umol, 1 eq) in NH₃/MeOH (7M, 3 mL) was stirred at 80° C.for 16 h in the sealed tube. Upon completion, the reaction mixture wasconcentrated under reduced pressure to give(2S,4S)—N-[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]-1-[(E)-3-(4-chloro-2-fluoro-phenyl)prop-2-enoyl]-4-phenyl-pyrrolidine-2-carboxamide(0.09 g, crude) as a yellow oil. MS (ESI) m/z 527.0 [M+H]⁺.

Step 6:(2S,4S)-1-((E)-3-(4-chloro-2-fluorophenyl)acryloyl)-N—((S)-1-cyano-2-((S)-2-oxopyrrolidin-3-yl)ethyl)-4-phenylpyrrolidine-2-carboxamide

To a solution of(2S,4S)—N-[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]-1-[(E)-3-(4-chloro-2-fluoro-phenyl)prop-2-enoyl]-4-phenyl-pyrrolidine-2-carboxamide(0.09 g, 170.78 umol, 1 eq) in DCM (1 mL) was added Burgess reagent(203.50 mg, 853.91 umol, 5 eq), the solution was stirred at 25° C. for 1h. Upon completion, the reaction mixture was concentrated under reducedpressure to give a residue. The residue was purified by prep-HPLC(column: Waters Xbridge BEH C18 100*25 mm*5 um; mobile phase: [water (10mM NH₄HCO₃)-ACN]; B %: 30%-60%, 10 min) to give(2S,4S)-1-[(E)-3-(4-chloro-2-fluoro-phenyl)prop-2-enoyl]-N-[(1S)-1-cyano-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]-4-phenyl-pyrrolidine-2-carboxamide(29.73 mg, 56.89 umol, 33.31% yield, 97.4% purity) as a solid. MS (ESI)m/z 509.1 [M+H]⁺.

¹H NMR (400 MHz, DMSO-d₆) δ=9.17-8.86 (m, 1H), 8.07-7.75 (m, 1H),7.75-7.65 (m, 1H), 7.62-7.49 (m, 2H), 7.48-7.30 (m, 5H), 7.26 (tt,J=3.0, 5.6 Hz, 1H), 7.22-6.73 (m, 1H), 5.09-4.83 (m, 1H), 4.69-4.47 (m,1H), 4.40-4.01 (m, 1H), 3.77-3.50 (m, 3H), 3.19-3.04 (m, 2H), 2.44-2.31(m, 2H), 2.22-2.09 (m, 2H), 1.88-1.59 (m, 2H).

Example 17. Synthesis of Viral Protease Inhibitor Compound 183

Step 1: methyl (2S)-2-amino-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate;hydrochloride

Methyl(2S)-2-(tert-butoxycarbonylamino)-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(300 mg, 1.05 mmol, 1 eq) was added HCl/EtOAc (4 M, 30 mL) at 25° C. Themixture was stirred at 25° C. for 1 h. The reaction mixture wasconcentrated under reduced pressure to give a product methyl(2S)-2-amino-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate:HCl (230 mg, crude)as an oil and used directly for next step.

Step 2: (S)-tert-butylS-(((S)-1-methoxy-1-oxo-3-((S)-2-oxopyrrolidin-3-yl)propan-2-yl)carbamoyl)-6-azaspiro[2.5]octane-6-carboxylate

A mixture of methyl (2S)-2-amino-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(230 mg, 1.03 mmol, 1 eq, HCl),(7S)-6-tert-butoxycarbonyl-6-azaspiro[2.5]octane-7-carboxylic acid(263.72 mg, 1.03 mmol, 1 eq), T3P (657.31 mg, 2.07 mmol, 614.31 uL, 2eq), Et₃N (522.60 mg, 5.16 mmol, 718.85 uL, 5 eq) and DMF (5 mL) wasstirred at 25° C. for 1 h. The reaction mixture was diluted with H₂O (30mL) and extracted with DCM (30 mL*3). The combined organic layers werewashed with brine (50 mL), dried over Na₂SO₄, filtered and concentratedunder reduced pressure to give a residue. The residue was purified bycolumn chromatography (SiO₂, petroleum ether/EtOAc=0/1) to get theproduct (S)-tert-butyl5-(((S)-1-methoxy-1-oxo-3-((S)-2-oxopyrrolidin-3-yl)propan-2-yl)carbamoyl)-6-azaspiro[2.5]octane-6-carboxylate(300 mg, 708.38 umol, 68.58% yield), as yellow oil. MS (ESI) m/z 424.1[M+H]⁺

Step 3: (S)-methyl3-((S)-2-oxopyrrolidin-3-yl)-2-((S)-6-azaspiro[2.5]octane-5-carboxamido)propanoate

A mixture of (S)-tert-butyl5-(((S)-1-methoxy-1-oxo-3-((S)-2-oxopyrrolidin-3-yl)propan-2-yl)carbamoyl)-6-azaspiro[2.5]octane-6-carboxylate(290 mg, 684.77 umol, 1 eq) and HCl/EtOAc (4 M, 30 mL) was stirred at25° C. for 1 h. The reaction mixture was concentrated under reducedpressure to give a product (S)-methyl3-((S)-2-oxopyrrolidin-3-yl)-2-((S)-6-azaspiro[2.5]octane-5-carboxamido)propanoate(240 mg, crude, HCl) as a an oil and used directly for next step.

Step 4: (S)-methyl2-((S)-6-(4-methoxy-1H-indole-2-carbonyl)-6-azaspiro[2.5]octane-5-carboxamido)-3-((S)-2-oxopyrrolidin-3-yl)propanoate

A mixture of (S)-methyl3-((S)-2-oxopyrrolidin-3-yl)-2-((S)-6-azaspiro[2.5]octane-5-carboxamido)propanoate(240 mg, 666.95 umol, 1 eq, HCl), 4-methoxy-1H-indole-2-carboxylic acid(127.51 mg, 666.95 umol, 1 eq), DMAP (162.96 mg, 1.33 mmol, 2 eq), EDCI(255.71 mg, 1.33 mmol, 2 eq), DMF (2 mL) and DCM (4 mL) was stirred at25° C. for 1 h. The reaction mixture was diluted with H₂O (30 mL) andextracted with DCM (30 mL*3). The combined organic layers were washedwith brine (50 mL), dried over Na₂SO₄, filtered and concentrated underreduced pressure to give a residue. The residue was purified by columnchromatography (SiO₂, petroleum ether/EtOAc=0/1) to get the compound(S)-methyl2-((S)-6-(4-methoxy-1H-indole-2-carbonyl)-6-azaspiro[2.5]octane-5-carboxamido)-3-((S)-2-oxopyrrolidin-3-yl)propanoate(150 mg, 275.74 umol, 41.34% yield, 91.28% purity) as an oil. MS (ESI)m/z 495.2 [M−H]⁻

Step 5:(S)-6-(4-methoxy-1H-indole-2-carbonyl)-6-azaspiro[2.5]octane-5-carboxylicacid

A mixture of (S)-methyl2-((S)-6-(4-methoxy-1H-indole-2-carbonyl)-6-azaspiro[2.5]octane-5-carboxamido)-3-((S)-2-oxopyrrolidin-3-yl)propanoate,LiOH (24.12 mg, 1.01 mmol, 5 eq), H₂O (1 mL) and THF (4 mL) was stirredat 25° C. for 16 h. The reaction mixture was concentrated under reducedpressure to give a product(S)-6-(4-methoxy-1H-indole-2-carbonyl)-6-azaspiro[2.5]octane-5-carboxylicacid (65 mg, crude) as a solid. MS (ESI) m/z 327.1 [M−H]⁻

Step 6: tert-butyl((S)-1-amino-1-oxo-3-((S)-2-oxopyrrolidin-3-yl)propan-2-yl)carbamate

A mixture of methyl(2S)-2-(tert-butoxycarbonylamino)-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(400 mg, 1.40 mmol, 1 eq) and NH₃/MeOH (7 M, 10 mL) was stirred at 80°C. for 16 h. The reaction mixture was concentrated under reducedpressure to give a product tert-butyl((S)-1-amino-1-oxo-3-((S)-2-oxopyrrolidin-3-yl)propan-2-yl)carbamate(380 mg, crude) as a solid.

Step 7: (S)-2-amino-3-((S)-2-oxopyrrolidin-3-yl)propanamide

A mixture of tert-butyl((S)-1-amino-1-oxo-3-((S)-2-oxopyrrolidin-3-yl)propan-2-yl)carbamate(300 mg, 1.11 mmol, 1 eq) and HCl/EtOAc (4 M, 15 mL, 54.26 eq) wasstirred at 25° C. for 0.5 h. The reaction mixture was concentrated underreduced pressure to give a product(S)-2-amino-3-((S)-2-oxopyrrolidin-3-yl)propanamide (190 mg, crude) as asolid and used directly for next step.

Step 8:(S)—N—((S)-1-amino-1-oxo-3-((S)-2-oxopyrrolidin-3-yl)propan-2-yl)-6-(4-methoxy-1H-indole-2-carbonyl)-6-azaspiro[2.5]octane-5-carboxamide

A solution of(S)-6-(4-methoxy-1H-indole-2-carbonyl)-6-azaspiro[2.5]octane-5-carboxylicacid (65 mg, 197.95 umol, 1 eq),(S)-2-amino-3-((S)-2-oxopyrrolidin-3-yl)propanamide (33.89 mg, 197.95umol, 1 eq), DMAP (48.37 mg, 395.91 umol, 2 eq), EDCI (75.90 mg, 395.91umol, 2 eq), DMF (1 mL) and DCM (3 mL) was stirred at 25° C. for 16 h.The reaction mixture was diluted with H₂O (30 mL) and extracted with DCM(30 mL*3). The combined organic layers were washed with brine (50 mL),dried over Na₂SO₄, filtered and concentrated under reduced pressure togive a residue. The residue was purified by prep-HPLC (column:Phenomenex Gemini-NX C18 75*30 mm*3 um; mobile phase:

[water (0.05% NH₃H₂O+10 mM NH₄HCO₃)-ACN]; B %: 10%-40%, 8 min) to getthe compound(S)—N—((S)-1-amino-1-oxo-3-((S)-2-oxopyrrolidin-3-yl)propan-2-yl)-6-(4-methoxy-1H-indole-2-carbonyl)-6-azaspiro[2.5]octane-5-carboxamide(45 mg, 79.43 umol, 40.13% yield, 85% purity) as a solid. MS (ESI) m/z480.2 [M−H]⁻

Step 9:(S)—N—((S)-1-cyano-2-((S)-2-oxopyrrolidin-3-yl)ethyl)-6-(4-methoxy-1H-indole-2-carbonyl)-6-azaspiro[2.5]octane-5-carboxamide

A mixture of(S)—N—((S)-1-amino-1-oxo-3-((S)-2-oxopyrrolidin-3-yl)propan-2-yl)-6-(4-methoxy-1H-indole-2-carbonyl)-6-azaspiro[2.5]octane-5-carboxamide(40 mg, 83.07 umol, 1 eq), Burgess reagent (237.55 mg, 996.80 umol, 12eq) and DCM (20 mL) was stirred at 25° C. for 8 h. The reaction mixturewas concentrated under reduced pressure to give a residue. The residuewas purified by prep-HPLC (column: Phenomenex Gemini-NX C18 75*30 mm*3um; mobile phase: [water (0.05% NH₃H₂O+10 mM NH₄HCO₃)-ACN]; B %:20%-40%, 8 min) to get the product(S)—N—((S)-1-cyano-2-((S)-2-oxopyrrolidin-3-yl)ethyl)-6-(4-methoxy-1H-indole-2-carbonyl)-6-azaspiro[2.5]octane-5-carboxamide(17 mg, 34.79 umol, 41.89% yield, 94.87% purity), as a solid. MS (ESI)m/z 462.2 [M−H]⁻.

¹H NMR (400 MHz, DMSO-d₆) δ=11.64 (s, 1H), 9.26-8.52 (m, 1H), 7.87-7.61(m, 1H), 7.18-7.07 (m, 1H), 7.06-6.96 (m, 1H), 6.85-6.60 (m, 1H), 6.51(d, 1H), 5.30-4.93 (m, 2H), 4.61-4.41 (m, 1H), 3.85 (s, 3H), 3.21-2.96(m, 2H), 2.39-2.03 (m, 5H), 1.96-1.56 (m, 4H), 0.99 (d, 1H), 0.45-0.15(m, 4H)

Example 18. Synthesis of Viral Protease Inhibitor Compound 185

Step 1: (S)-methyl2-((S)-2-((tert-butoxycarbonyl)amino)-3-cyclohexylpropanamido)-3-((S)-2-oxopyrrolidin-3-yl)propanoate

To a solution of methyl(2S)-2-amino-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate (170 mg, 763.47umol, 1 eq, HCl) and(2S)-2-(tert-butoxycarbonylamino)-3-cyclohexyl-propanoic acid (207.17mg, 763.47 umol, 1 eq) in DMF (2 mL) was added DMAP (186.55 mg, 1.53mmol, 2 eq) and EDCI (292.71 mg, 1.53 mmol, 2 eq). The mixture was addedDCM (3 mL) and stirred at 25° C. for 2 h. The reaction mixture wasquenched by addition H₂O (30 mL) at 0° C., and then extracted with DCM(20 mL*3). The combined organic layers were washed with brine, driedover Na₂SO₄, filtered and concentrated under reduced pressure to give aresidue. The residue was purified by prep-TLC (SiO₂, petroleumether/EtOAc=0/1) to get the product methyl(2S)-2-[[(2S)-2-(tert-butoxycarbonylamino)-3-cyclohexyl-propanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(250 mg, 568.77 umol, 74.50% yield) was obtained as a solid. MS (ESI)m/z 440.3 [M+H]⁺

Step 2: (S)-methyl2-((S)-2-amino-3-cyclohexylpropanamido)-3-((S)-2-oxopyrrolidin-3-yl)propanoate

A solution of methyl(2S)-2-[[(2S)-2-(tert-butoxycarbonylamino)-3-cyclohexyl-propanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(200 mg, 455.02 umol, 1 eq) in EtOAc (0.5 mL) was added drop-wiseHCl/EtOAc (4 M, 2.00 mL, 17.58 eq) at 25° C. The mixture was stirred at25° C. for 1 h. The reaction mixture was concentrated under reducedpressure to give a product methyl(2S)-2-[[(2S)-2-amino-3-cyclohexyl-propanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(150 mg, crude, HCl) was obtained as a solid and used directly nextstep. MS (ESI) m/z 340.1 [M+H]⁺

Step 3:((S)-methyl2-((S)-3-cyclohexyl-2-(4-methoxy-1H-indole-2-carboxamido)propanamido)-3-((S)-2-oxopyrrolidin-3-yl)propanoate

A solution of 4-methoxy-1H-indole-2-carboxylic acid (99.18 mg, 518.77umol, 1.3 eq) and methyl(2S)-2-[[(2S)-2-amino-3-cyclohexyl-propanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(150 mg, 399.05 umol, 1 eq, HCl) in DMF (2 mL) was added DMAP (97.50 mg,798.11 umol, 2.0 eq) and EDCI (153.00 mg, 798.11 umol, 2 eq). Themixture was added DCM (4 mL) and stirred at 25° C. for 2 h. The reactionmixture was quenched by addition H₂O (20 mL) at 0° C., and thenextracted with DCM (20 mL*3). The combined organic layers were washedwith brine (20 mL), dried over Na₂SO₄, filtered and concentrated underreduced pressure to give a residue. The residue was purified by columnchromatography (SiO₂, DCM:MeOH=1:0 to 10:1) to get a product methyl(2S)-2-[[(2S)-3-cyclohexyl-2-[(4-methoxy-1H-indole-2-carbonyl)amino]propanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(150 mg, 292.63 umol, 73.33% yield) was obtained as a solid.

¹H NMR (METHANOL-d₄, 400 MHz): δ ppm 7.26 (s, 1H), 7.09-7.20 (m, 1H),7.02 (d, J=8.3 Hz, 1H), 6.51 (d, J=7.6 Hz, 1H), 4.66 (br dd, J=9.0, 6.3Hz, 1H), 4.52-4.58 (m, 1H), 3.93 (s, 3H), 3.72 (s, 3H), 3.22-3.29 (m,2H), 2.54-2.62 (m, 1H), 2.26-2.33 (m, 1H), 2.15-2.23 (m, 1H), 1.66-1.87(m, 9H), 1.47-1.54 (m, 1H), 1.25-1.40 (m, 3H), 0.96-1.06 (m, 2H)

Step 4:N—((S)-1-(((S)-1-amino-1-oxo-3-((S)-2-oxopyrrolidin-3-yl)propan-2-yl)amino)-3-cyclohexyl-1-oxopropan-2-yl)-4-methoxy-1H-indole-2-carboxamide

To a solution of methyl(2S)-2-[[(2S)-3-cyclohexyl-2-[(4-methoxy-1H-indole-2-carbonyl)amino]propanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(150 mg, 292.63 umol, 1 eq) in ammonia (15.30 g, 898.39 mmol, 15.00 mL,3070.07 eq) was heated to 80° C. for 12 h in a sealed tube. The reactionmixture was concentrated under reduced pressure to get a productN-[(1S)-2-[[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]amino]-1-(cyclohexylmethyl)-2-oxo-ethyl]-4-methoxy-1H-indole-2-carboxamide(140 mg, crude) was obtained as a solid. MS (ESI) m/z 498.2 [M+H]⁺

¹H NMR (METHANOL-d₄, 400 MHz): δ ppm 7.27-7.34 (m, 1H), 7.13-7.20 (m,1H), 7.05 (d, J=8.3 Hz, 1H), 6.53 (d, J=7.7 Hz, 1H), 4.62 (t, J=7.6 Hz,1H), 4.42-4.51 (m, 1H), 3.95 (s, 3H), 3.22-3.30 (m, 2H), 2.53 (td,J=9.2, 4.5 Hz, 1H), 2.33 (ddd, J=9.2, 6.4, 3.4 Hz, 1H), 2.17 (ddd,J=14.1, 11.4, 4.6 Hz, 1H), 1.71-1.88 (m, 9H), 1.46-1.53 (m, 1H),1.21-1.32 (m, 3H), 0.97-1.09 (m, 2H)

Step 5:N—((S)-1-(((S)-1-amino-1-oxo-3-((S)-2-oxopyrrolidin-3-yl)propan-2-yl)amino)-3-cyclohexyl-1-oxopropan-2-yl)-4-methoxy-1H-indole-2-carboxamide

To a solution ofN-[(1S)-2-[[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]amino]-1-(cyclohexylmethyl)-2-oxo-ethyl]-4-methoxy-1H-indole-2-carboxamide(80 mg, 160.78 umol, 1 eq) in DCM (3 mL) was added Burgess reagent(114.94 mg, 482.33 umol, 3 eq), then the mixture was stirred at 25° C.for 3 h. The reaction mixture was concentrated under reduced pressure togive a residue. The residue was purified by neutral prep-HPLC to get aproductN-[(1S)-2-[[(1S)-1-cyano-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]amino]-1-(cyclohexylmethyl)-2-oxo-ethyl]-4-methoxy-1H-indole-2-carboxamide(20.02 mg, 41.75 umol, 25.97% yield, 100% purity) was obtained as asolid. MS (ESI) m/z 480.1 [M+H]⁺.

Prep-HPLC condition: column: Waters Xbridge BEH C18 100*25 mm*5 um;mobile phase: [water (10 mM NH₄HCO₃)-ACN]; B %: 30%-60%, 10 min

¹H NMR (METHANOL-d₄, 400 MHz): δ ppm 7.28 (s, 1H), 7.11-7.18 (m, 1H),7.02 (d, J=8.3 Hz, 1H), 6.51 (d, J=7.6 Hz, 1H), 5.05 (dd, J=10.1, 5.9Hz, 1H), 4.56-4.61 (m, 1H), 3.93 (s, 3H), 3.22-3.30 (m, 2H), 2.55-2.66(m, 1H), 2.23-2.40 (m, 2H), 1.65-1.94 (m, 9H), 1.41-1.52 (m, 1H),1.17-1.36 (m, 3H), 0.94-1.10 (m, 2H).

Example 19. Synthesis of Viral Protease Inhibitor Compound 197

Step 1: methyl (2S)-2-amino-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate

To a mixture of methyl(2S)-2-(tert-butoxycarbonylamino)-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(500 mg, 1.75 mmol, 1 eq) in HCl/EtOAc (4M, 20 mL). The mixture wasstirred at 25° C. and stirred for 1 h. Once the reaction was completed,the reaction was concentrated to give the crude methyl(2S)-2-amino-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate (400 mg, crude, anoil). The crude product was used directly without further purification.MS (ESI) m/z 187.1 [M+H]⁺

Step 2: tert-butyl(2S,5S)-2-[[(1S)-2-methoxy-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]carbamoyl]-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-3-carboxylate

To a mixture of methyl(2S)-2-amino-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate (230 mg, 1.24 mmol,1 eq) and(2S,5S)-3-tert-butoxycarbonyl-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxylicacid (315.35 mg, 1.24 mmol, 1 eq) in DCM (4.5 mL) and DMF (1.5 mL) wasadded EDCI (473.57 mg, 2.47 mmol, 2 eq) and DMAP (301.80 mg, 2.47 mmol,2 eq). The mixture was stirred at 25° C. for 2 h. Once the reaction wascompleted, the reaction was concentrated and purified by prep-HPLC(column: Waters Xbridge BEH C18 100*30 mm*10 um; mobile phase: [water(10 mM NH₄HCO₃)-ACN]; B %: 25%-55%, 10 min) to give tert-butyl(2S,5S)-2-[[(1S)-2-methoxy-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]carbamoyl]-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-3-carboxylate(200 mg, 425.03 umol, 34.41% yield, 90% purity) (solid). MS (ESI) m/z424.1 [M+H]⁺

Step 3: (S)-methyl2-((1S,2S,5S)-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamido)-3-((S)-2-oxopyrrolidin-3-yl)propanoate

To a mixture of (1S,2S,5S)-tert-butyl2-(((S)-1-methoxy-1-oxo-3-((S)-2-oxopyrrolidin-3-yl)propan-2-yl)carbamoyl)-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-3-carboxylate(200 mg, 236.13 umol, 50% purity, 1 eq) in HCl/EtOAc (4M, 20 mL). Themixture was stirred at 25° C. and stirred for 2 h. Once the reaction wascompleted, the reaction was concentrated to give the crude (S)-methyl2-((1S,2S,5S)-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamido)-3-((S)-2-oxopyrrolidin-3-yl)propanoate(150 mg, crude, an oil). Crude product was used directly without furtherpurification. MS (ESI) m/z 324.1 [M+H]⁺

Step 4: methyl(2S)-2-[[(2S,5S)-3-(4-methoxy-1H-indole-2-carbonyl)-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carbonyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate

To a mixture of (S)-methyl2-((1S,2S,5S)-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamido)-3-((S)-2-oxopyrrolidin-3-yl)propanoate(150 mg, 463.84 umol, 1 eq) and 4-methoxy-1H-indole-2-carboxylic acid(88.68 mg, 463.84 umol, 1 eq) in DCM (3 mL) and DMF (1 mL) was addedEDCI (177.84 mg, 927.68 umol, 2 eq) and DMAP (113.33 mg, 927.68 umol, 2eq). The mixture was stirred at 25° C. and stirred for 14 h. Once thereaction was completed, the mixture was poured into water (50 mL) andextracted with DCM (20 mL*3). The combined organic phase was washed withbrine (60 mL*3), dried with anhydrous Na₂SO₄, filtered and concentratedin vacuum. The residue was purified by silica gel chromatography (columnheight: 250 mm, diameter: 100 mm, 100-200 mesh silica gel, petroleumether/ethyl acetate=1/1, 0/1) to afford methyl(2S)-2-[[(2S,5S)-3-(4-methoxy-1H-indole-2-carbonyl)-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carbonyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(50 mg, 80.56 umol, 17.37% yield, 80% purity) as solid. MS (ESI) m/z497.2 [M+H]⁺

Step 5:(2S,5S)—N-[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]-3-(4-methoxy-1H-indole-2-carbonyl)-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide

To a mixture of methyl(2S)-2-[[(2S,5S)-3-(4-methoxy-1H-indole-2-carbonyl)-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carbonyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(100 mg, 201.39 umol, 1 eq) in ammonia (5.10 g, 299.46 mmol, 5 mL,1486.99 eq). The mixture was stirred at 80° C. and stirred for 16 h.Once the reaction was completed, the reaction was concentrated to givethe crude(2S,5S)—N-[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]-3-(4-methoxy-1H-indole-2-carbonyl)-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide(100 mg, crude) (solid). Crude product was used directly without furtherpurification. MS (ESI) m/z 482.3[M+H]⁺

Step 6:(2S,5S)—N-[(1S)-1-cyano-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]-3-(4-methoxy-1H-indole-2-carbonyl)-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide

To a mixture of(2S,5S)—N-[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]-3-(4-methoxy-1H-indole-2-carbonyl)-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide(50 mg, 103.83 umol, 1 eq) in DCM (3 mL) was addedmethoxycarbonyl-(triethylammonio)sulfonyl-azanide (49.49 mg, 207.67umol, 2 eq). The mixture was stirred at 25° C. for 2 h. Once thereaction was completed, the reaction was concentrated and purified byprep-HPLC (column: Phenomenex Gemini-NX 80*40 mm*3 um; mobile phase:[water (10 mM NH4HCO3)-ACN]; B %: 20%-40%, 8 min) to give(2S,5S)—N-[(1S)-1-cyano-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]-3-(4-methoxy-1H-indole-2-carbonyl)-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide(14.44 mg, 31.15 umol, 30.00% yield, 100% purity) as a solid. MS (ESI)m/z 464.2[M+H]⁺.

1H NMR (400 MHz, METHANOL-d4): δ ppm 7.16-7.18 (m, 1H), 7.11-7.14 (m,2H), 6.4-6.88 (m, 1H), 5.05-5.08 (m, 0.5H), 4.06 (s, 2H), 3.94-3.98 (m,0.5H), 3.77-3.86 (m, 4H), 3.28 (s, 2H), 2.61-3.69 (m, 1H), 2.27-2.32 (m,1H), 2.25-2.26 (m, 1H), 1.78-2.00 (m, 1H), 1.74-1.75 (m, 1H) 1.35-1.64(m, 2H), 0.97-1.15 (m, 6H)

Example 20. Synthesis of Viral Protease Inhibitor Compound 213

Step 1: (S)-Methyl 2-amino-3-((S)-2-oxopyrrolidin-3-yl)propanoate

Methyl(2S)-2-(tert-butoxycarbonylamino)-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(501 mg, 1.75 mmol, 1 eq) in HCl/EtOAc (4 M, 10.02 mL, 22.91 eq) wasstirred at 25° C. for 1 h. Upon completion, the solution wasconcentrated. The crude was used to next step directly and withoutfurther purification. Methyl (2S)-2-amino-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate (300 mg, crude) was obtained as yellow oil.

Step 2: (S)-benzyl3-(((S)-1-methoxy-1-oxo-3-((S)-2-oxopyrrolidin-3-yl)propan-2-yl)carbamoyl)tetrahydropyridazine-1(2H)-carboxylate

Methyl (2S)-2-amino-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate (295.93 mg,1.59 mmol, 1.4 eq) and(3S)-1-benzyloxycarbonylhexahydropyridazine-3-carboxylic acid (300 mg,1.14 mmol, 1 eq) in DCM (2 mL)/THF (2 mL) was cooled to 0° C., then theT3P (1.08 g, 1.70 mmol, 1.01 mL, 50% purity, 1.5 eq) and DIEA (440.14mg, 3.41 mmol, 593.18 uL, 3 eq) was added and the solution was stirredat 25° C. for 13 h. Upon completion, the solution was diluted with H₂O(20 mL), extracted with Ethyl acetate (30 mL*3), the combined organicphase was dried over Na₂SO₄, filtrated and concentrated to give thecrude. The crude was used to next step directly and without furtherpurification. Benzyl(3S)-3-[[(1S)-2-methoxy-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl] methyl]ethyl] carbamoyl] hexahydropyridazine-1-carboxylate (455 mg, crude) wasobtained as yellow oil. MS (ESI) m/z 433.1 [M+H]⁺.

Step 3: (S)-benzyl2-((E)-3-(4-chloro-2-fluorophenyl)acryloyl)-3-(((S)-1-methoxy-1-oxo-3-((S)-2-oxopyrrolidin-3-yl)propan-2-yl)carbamoyl)tetrahydropyridazine-1(2H)-carboxylate

Benzyl(3S)-3-[[(1S)-2-methoxy-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]carbamoyl]hexahydropyridazine-1-carboxylate(200 mg, 462.46 umol, 1 eq) in DCM (2 mL) was added the DIEA (119.54 mg,924.92 umol, 161.10 uL, 2 eq),(E)-3-(4-chloro-2-fluoro-phenyl)prop-2-enoyl chloride (121.56 mg, 554.95umol, 1.2 eq) was added and the solution was stirred at 25° C. for 1 h.Upon completion, the solution was diluted with H₂O (10 mL), extractedwith DCM (20 mL*3), the combined organic phase was dried over Na₂SO₄,filtrated and concentrated to give the crude. The residue was purifiedby prep-TLC (SiO₂, DCM:MeOH=10:1). Benzyl(3S)-2-[(E)-3-(4-chloro-2-fluoro-phenyl)prop-2-enoyl]-3-[[(1S)-2-methoxy-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl] ethyl] carbamoyl] hexahydropyridazine-1-carboxylate (160 mg,248.88 umol, 53.82% yield, 95.67% purity) was obtained as yellow oil. MS(ESI) m/z 433.1 [M+H]⁺.

Step 4: (S)-methyl2-((S)-2-((E)-3-(4-chloro-2-fluorophenyl)acryloyl)hexahydropyridazine-3-carboxamido)-3-((S)-2-oxopyrrolidin-3-yl)propanoate

Benzyl(3S)-2-[(E)-3-(4-chloro-2-fluoro-phenyl)prop-2-enoyl]-3-[[(1S)-2-methoxy-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]carbamoyl]hexahydropyridazine-1-carboxylate(160 mg, 260.14 umol, 1 eq) in TFA (5 mL) was stirred at 75° C. for 1 h.Upon completion, the solution was concentrated to remove the TFA,diluted with the solution of NaHCO₃, extracted with EtOAc (20 mL*3), thecombined organic phase was dried over Na₂SO₄, filtrated and concentratedto give the crude. The crude was used to next step directly and withoutfurther purification. Methyl(2S)-2-[[(3S)-2-[(E)-3-(4-chloro-2-fluoro-phenyl)prop-2-enoyl]hexahydropyridazine-3-carbonyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl] propanoate (80 mg, crude) wasobtained as solid. MS (ESI) m/z 481.0 [M+H]⁺.

Step 5:(S)—N—((S)-1-amino-1-oxo-3-((S)-2-oxopyrrolidin-3-yl)propan-2-yl)-2-((E)-3-(4-chloro-2-fluorophenyl)acryloyl)hexahydropyridazine-3-carboxamide

Methyl(2S)-2-[[(3S)-2-[(E)-3-(4-chloro-2-fluoro-phenyl)prop-2-enoyl]hexahydropyridazine-3-carbonyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(80 mg, 166.35 umol, 1 eq) in NH₃/MeOH (7 M, 4.00 mL, 168.32 eq) wasstirred at 80° C. for 17 h. Upon completion, the solution wasconcentrated to remove the MeOH. The crude was used to next stepdirectly and without further purification.(3S)—N-[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl] methyl]ethyl]-2-[(E)-3-(4-chloro-2-fluoro-phenyl) prop-2-enoyl]hexahydropyridazine-3-carboxamide (75 mg, crude) was obtained as yellowoil. MS (ESI) m/z 481.0 [M+H]⁺.

Step 6:(S)-2-((E)-3-(4-chloro-2-fluorophenyl)acryloyl)-N—((S)-1-cyano-2-((S)-2-oxopyrrolidin-3-yl)ethyl)hexahydropyridazine-3-carboxamide

(3S)—N-[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]-2-[(E)-3-(4-chloro-2-fluoro-phenyl)prop-2-enoyl]hexahydropyridazine-3-carboxamide(75 mg, 160.98 umol, 1 eq) in DCM (0.5 mL) was added the Burgess reagent(76.72 mg, 321.95 umol, 2 eq) and the solution was stirred at 25° C. for2 h. Upon completion, the solution was concentrated to remove the DCM.The residue was purified by prep-HPLC (neutral condition). Column:Phenomenex Gemini-NX 80*40 mm*3 um; mobile phase: [water (10 mMNH4HCO3)-ACN]; B %: 25%-45%, 8 min.(3S)-2-[(E)-3-(4-chloro-2-fluoro-phenyl)prop-2-enoyl]-N-[(1S)-1-cyano-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]hexahydropyridazine-3-carboxamide(20 mg, 44.65 umol, 27.74% yield, 100% purity) was obtained as a solid.¹H NMR (400 MHz, METHANOL-d₄) δ=7.79-7.60 (m, 3H), 7.32-7.22 (m, 2H),5.17 (dd, J=2.2, 6.0 Hz, 1H), 5.07 (dd, J=6.4, 9.7 Hz, 1H), 3.38-3.32(m, 2H), 3.12 (br d, J=13.7 Hz, 1H), 2.90-2.74 (m, 1H), 2.56 (dq, J=5.8,9.0 Hz, 1H), 2.44-2.14 (m, 3H), 2.08-1.79 (m, 3H), 1.75-1.53 (m, 2H). MS(ESI) m/z 448.2 [M+H]⁺.

Step 7. (E)-3-(4-chloro-2-fluorophenyl)acryloyl chloride

(E)-3-(4-chloro-2-fluoro-phenyl)prop-2-enoic acid (120 mg, 598.22 umol,1 eq) in DCM (0.5 mL) was added the DMF (437.26 ug, 5.98 umol, 0.46 uL,0.01 eq) and cooled to 0° C., then the (COCl)₂ (151.86 mg, 1.20 mmol,104.73 uL, 2 eq) was added and the solution was stirred at 25° C. for 1h. Upon completion, the solution was concentrated to remove the DCM andgive the crude. The crude was used to next step directly and withoutfurther purification. (E)-3-(4-chloro-2-fluoro-phenyl)prop-2-enoylchloride (125 mg, crude) was obtained as a solid.

Example 21. Synthesis of Viral Protease Inhibitor Compound 201

Step 1: methyl (2S)-2-amino-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate;hydrochloride

Methyl(2S)-2-(tert-butoxycarbonylamino)-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(250 mg, 873.14 umol, 1 eq) was added HCl/EtOAc (4 M, 30 mL) at 25° C.The mixture was stirred at 25° C. for 1 h. The reaction mixture wasconcentrated under reduced pressure to give a product methyl(2S)-2-amino-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate; hydrochloride (200mg, crude) as a solid and used directly for next step.

Step 2:(S)-methyl-2-((S)-2-((tert-butoxycarbonyl)amino)pent-4-ynamido)-3-((S)-2-oxopyrrolidin-3-yl)propanoate

A mixture of methyl(2S)-2-amino-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate; hydrochloride (180mg, 808.38 umol, 1 eq), (2S)-2-(tert-butoxycarbonylamino)pent-4-ynoicacid (172.37 mg, 808.38 umol, 1 eq), TEA (572.59 mg, 5.66 mmol, 787.61uL, 7 eq), T3P (1.03 g, 1.62 mmol, 961.53 uL, 50% purity, 2 eq) and DMF(3 mL) was stirred at 25° C. for 1 h. The reaction mixture was dilutedwith H₂O (30 mL) and extracted with DCM (30 mL*3). The combined organiclayers were washed with brine (50 mL), dried over Na₂SO₄, filtered andconcentrated under reduced pressure to give a residue. The residue waspurified by column chromatography (SiO₂, petroleum ether/EtOAc=0/1) toafford the product(S)-methyl-2-((S)-2-((tert-butoxycarbonyl)amino)pent-4-ynamido)-3-((S)-2-oxopyrrolidin-3-yl)propanoate(150 mg, 393.26 umol, 48.65% yield), as an oil. MS (ESI) m/z 382.1[M+H]⁺

Step 3: (S)-methyl2-((S)-2-aminopent-4-ynamido)-3-((S)-2-oxopyrrolidin-3-yl)propanoate

A mixture of(S)-methyl-2-((S)-2-((tert-butoxycarbonyl)amino)pent-4-ynamido)-3-((S)-2-oxopyrrolidin-3-yl)propanoate(140 mg, 367.05 umol, 1 eq) and HCl/EtOAc (4 M, 30 mL) was stirred at25° C. for 1 h. The reaction mixture was concentrated under reducedpressure to give a product (S)-methyl2-((S)-2-aminopent-4-ynamido)-3-((S)-2-oxopyrrolidin-3-yl)propanoate(120 mg, crude, HCl) as an oil and used directly for next step.

Step 4:(S)-methyl-2-((S)-2-(4-methoxy-1H-indole-2-carboxamido)pent-4-ynamido)-3-((S)-2-oxopyrrolidin-3-yl)propanoate

A mixture of (S)-methyl2-((S)-2-aminopent-4-ynamido)-3-((S)-2-oxopyrrolidin-3-yl)propanoate(120 mg, 377.63 umol, 1 eq, HCl), 4-methoxy-1H-indole-2-carboxylic acid(72.20 mg, 377.63 umol, 1 eq), EDCI (144.78 mg, 755.27 umol, 2 eq), DMAP(92.27 mg, 755.27 umol, 2 eq), DMF (2 mL) and DCM (4 mL) was stirred at25° C. for 1 h. The reaction mixture was diluted with H₂O (30 mL) andextracted with DCM (30 mL*3). The combined organic layers were washedwith brine (50 mL), dried over Na₂SO₄, filtered and concentrated underreduced pressure to give a residue. The residue was purified by columnchromatography (SiO₂, petroleum ether/EtOAc=0/1) to get the compound(S)-methyl-2-((S)-2-(4-methoxy-1H-indole-2-carboxamido)pent-4-ynamido)-3-((S)-2-oxopyrrolidin-3-yl)propanoate(90 mg, 160.56 umol, 42.52% yield, 81.08% purity), as an oil. MS (ESI)m/z 455.1 [M+H]⁺

Step 5:N—((S)-1-(((S)-1-amino-1-oxo-3-((S)-2-oxopyrrolidin-3-yl)propan-2-yl)amino)-1-oxopent-4-yn-2-yl)-4-methoxy-1H-indole-2-carboxamide

A mixture of(S)-methyl-2-((S)-2-(4-methoxy-1H-indole-2-carboxamido)pent-4-ynamido)-3-((S)-2-oxopyrrolidin-3-yl)propanoate(85 mg, 187.03 umol, 1 eq) and NH₃/MeOH (7 M, 10 mL) was stirred at 80°C. for 16 h. The reaction mixture was concentrated under reducedpressure to give a productN—((S)-1-(((S)-1-amino-1-oxo-3-((S)-2-oxopyrrolidin-3-yl)propan-2-yl)amino)-1-oxopent-4-yn-2-yl)-4-methoxy-1H-indole-2-carboxamide(85 mg, crude) as a solid. MS (ESI) m/z 440.2 [M+H]⁺

Step 6:N—((S)-1-(((S)-1-cyano-2-((S)-2-oxopyrrolidin-3-yl)ethyl)amino)-1-oxopent-4-yn-2-yl)-4-methoxy-1H-indole-2-carboxamide

A mixture ofN—((S)-1-(((S)-1-amino-1-oxo-3-((S)-2-oxopyrrolidin-3-yl)propan-2-yl)amino)-1-oxopent-4-yn-2-yl)-4-methoxy-1H-indole-2-carboxamide(80 mg, 182.04 umol, 1 eq), Burgess reagent (216.91 mg, 910.20 umol, 5eq) and DCM (5 mL) was stirred at 25° C. for 4 h. The reaction mixturewas concentrated under reduced pressure to give a residue. The residuewas purified by prep-HPLC (column: Waters Xbridge BEH C18 100*30 mm*10um; mobile phase: [water (0.04% NH₃H₂O+10 mM NH₄HCO₃)-ACN]; B %:20%-50%, 10 min) to get the productN—((S)-1-(((S)-1-cyano-2-((S)-2-oxopyrrolidin-3-yl)ethyl)amino)-1-oxopent-4-yn-2-yl)-4-methoxy-1H-indole-2-carboxamide(20 mg, 47.46 umol, 26.07% yield, 100% purity), as solid. MS (ESI) m/z422.2 [M+H]⁺.

¹H NMR (400 MHz, DMSO-d₆) δ=11.61 (d, J=1.8 Hz, 1H), 9.18-8.93 (m, 1H),8.74-8.58 (m, 1H), 7.78-7.62 (m, 1H), 7.37-7.29 (m, 1H), 7.15-7.07 (m,1H), 7.05-6.97 (m, 1H), 6.51 (d, J=7.5 Hz, 1H), 5.03-4.91 (m, 1H),4.65-4.50 (m, 1H), 3.89 (s, 3H), 3.20-3.05 (m, 2H), 2.91-2.85 (m, 1H),2.78-2.59 (m, 2H), 2.43-2.29 (m, 1H), 2.21-2.06 (m, 2H), 1.88-1.59 (m,2H)

Example 22. Synthesis of Viral Protease Inhibitor Compound 205

Step 1: (S)-2-((tert-butoxycarbonyl)amino)-3-cyclopropylpropanoic acid

To a solution of (2S)-2-amino-3-cyclopropyl-propanoic acid (1 g, 7.74mmol, 1 eq) in THF (5 mL) and H₂O (5 mL), was added K₂CO₃ (3.75 g, 27.10mmol, 3.5 eq) and (BoC)₂O (2.20 g, 10.07 mmol, 2.31 mL, 1.3 eq).Additional water was added to the mixture, and then the mixture wasstirred at 25° C. for 16 h. The organic solvent was then evaporated andthe aqueous solution was washed with petroleum ether (10 mL) andacidified to pH ˜3 with 1N aqueous citric acid (30 mL). The solution wasextracted with DCM (30 mL*3) and was concentrated in vacuum to afford(S)-2-((tert-butoxycarbonyl) amino)-3-cyclopropyl propanoic acid (1.8 g,crude) as an oil.

Step 2: (S)-methyl 2-amino-3-((S)-2-oxopyrrolidin-3-yl)propanoate

(S)-methyl 2-((tert-butoxycarbonyl) amino)-3-((S)-2-oxopyrrolidin-3-yl)propanoate (500 mg, 1.75 mmol, 1 eq) was added HCl/EtOAc (4 M, 5 mL) at25° C. The mixture was stirred at 25° C. for 1 h. The reaction mixturewas concentrated under reduced pressure to give a product (S)-methyl2-amino-3-((S)-2-oxopyrrolidin-3-yl) propanoate (350 mg, HCl, crude) asa yellow gum and used to next step directly.

Step 3:(S)-methyl2-((S)-2-((tert-butoxycarbonyl)amino)-3-cyclopropylpropanamido)-3-((S)-2-oxopyrrolidin-3-yl)propanoate

To a mixture of (S)-methyl 2-amino-3-((S)-2-oxopyrrolidin-3-yl)propanoate (250 mg, 1.12 mmol, 1 eq, HCl) and(S)-2-((tert-butoxycarbonyl) amino)-3-cyclopropyl propanoic acid (386.12mg, 1.68 mmol, 1.5 eq) in DCM (5 mL) was added TEA (568.05 mg, 5.61mmol, 781.36 uL, 5 eq) at 0° C., the mixture was added T3P (2.14 g, 3.37mmol, 2.00 mL, 50% purity, 3 eq) at 0° C., then the mixture was stirredat 25° C. for 2 h. The reaction mixture was quenched by water (10 mL)and was extracted with DCM (5 mL*3). The resulting solution was driedwith Na₂SO₄, filtered and concentration in vacuum to give a residue. Theresidue was purified by column chromatography (SiO₂, petroleumether:EtOAc=1:0 to 0:1) to afford the product (S)-methyl2-((S)-2-((tert-butoxycarbonyl)amino)-3-cyclopropylpropanamido)-3-((S)-2-oxopyrrolidin-3-yl)propanoate(400 mg, 905.74 umol, 80.67% yield, 90% purity) was obtained as a gum.

¹H NMR (400 MHz, CDCl₃) δ ppm 7.60 (d, J=5.6 Hz, 1H), 5.96 (s, 1H), 5.24(d, J=7.5 Hz, 1H), 4.65-4.47 (m, 1H), 4.24 (d, J=6.6 Hz, 1H), 3.73 (s,3H), 3.44-3.27 (m, 2H), 2.51-2.36 (m, 2H), 2.25-2.13 (m, 1H), 1.98-1.82(m, 1H), 1.66-1.58 (m, 1H), 1.44 (s, 9H), 1.30-1.21 (m, 1H), 0.86-0.71(m, 1H), 0.49 (d, J=7.9 Hz, 2H), 0.13 (d, J=4.4 Hz, 2H).

Step 4: (S)-methyl2-((S)-2-amino-3-cyclopropylpropanamido)-3-((S)-2-oxopyrrolidin-3-yl)propanoate

A solution of(S)-methyl2-((S)-2-((tert-butoxycarbonyl)amino)-3-cyclopropylpropanamido)-3-((S)-2-oxopyrrolidin-3-yl)propanoatein HCl/EtOAc (4M, 4 mL), the mixture was stirred at 25° C. for 1 h. Thereaction mixture was concentrated under reduced pressure to give aproduct (S)-methyl2-((S)-2-amino-3-cyclopropylpropanamido)-3-((S)-2-oxopyrrolidin-3-yl)propanoate (330 mg, crude, HCl) as a yellow gum and used directly nextstep.

1H NMR (400 MHz, MeOD-d₄) δ ppm 4.57 (dd, J=4.1, 11.0 Hz, 1H), 3.94 (t,J=6.7 Hz, 1H), 3.73 (s, 3H), 3.40-3.33 (m, 2H), 2.55-2.33 (m, 2H),2.19-2.07 (m, 1H), 2.03-2.00 (m, 1H), 1.93-1.84 (m, 2H), 1.24 (t, J=7.1Hz, 1H), 0.89-0.79 (m, 1H), 0.59 (dd, J=4.5, 7.9 Hz, 2H), 0.26-0.17 (m,2H).

Step 5:(S)-methyl2-((S)-3-cyclopropyl-2-(4-methoxy-1H-indole-2-carboxamido)propanamido)-3-((S)-2-oxopyrrolidin-3-yl)propanoate

To a mixture of 4-methoxy-1H-indole-2-carboxylic acid (257.73 mg, 1.35mmol, 1.5 eq) and (S)-methyl2-((S)-2-amino-3-cyclopropylpropanamido)-3-((S)-2-oxopyrrolidin-3-yl)propanoate (300 mg, 898.71 umol, 1 eq, HCl) in DCM (8 mL) was added EDCI(861.43 mg, 4.49 mmol, 5 eq) and DMAP (329.38 mg, 2.70 mmol, 3 eq), thenthe mixture was stirred at 25° C. for 2 h. The combined organic layerswere quenched with water (10 mL) and were extracted with DCM (4 mL*3).The resulting solution was dried over Na₂SO₄, filtered and concentratedunder reduced pressure to give a residue. The residue was purified bycolumn chromatography (SiO₂, EtOAc) to get the compound(S)-methyl2-((S)-3-cyclopropyl-2-(4-methoxy-1H-indole-2-carboxamido)propanamido)-3-((S)-2-oxopyrrolidin-3-yl)propanoate(250 mg, 425.06 umol, 47.30% yield, 80% purity) as yellow oil. MS (ESI)m/z 471.1 [M+H]⁺

Step 6:N—((S)-1-(((S)-1-amino-1-oxo-3-((S)-2-oxopyrrolidin-3-yl)propan-2-yl)amino)-3-cyclopropyl-1-oxopropan-2-yl)-4-methoxy-1H-indole-2-carboxamide

(S)-Methyl2-((S)-3-cyclopropyl-2-(4-methoxy-1H-indole-2-carboxamido)propanamido)-3-((S)-2-oxopyrrolidin-3-yl)propanoate(250 mg, 531.33 umol, 1 eq) was added with NH₃/MeOH (7M, 6.00 mL). Themixture was stirred at 80° C. for 16 h. The resulting mixture wasconcentrated under reduced pressure to give a residueN—((S)-1-(((S)-1-amino-1-oxo-3-((S)-2-oxopyrrolidin-3-yl)propan-2-yl)amino)-3-cyclopropyl-1-oxopropan-2-yl)-4-methoxy-1H-indole-2-carboxamide(200 mg, crude) as a solid. MS (ESI) m/z 456.1 [M+H]⁺

Step 7:N—((S)-1-(((S)-1-cyano-2-((S)-2-oxopyrrolidin-3-yl)ethyl)amino)-3-cyclopropyl-1-oxopropan-2-yl)-4-methoxy-1H-indole-2-carboxamide

To a mixture ofN—((S)-1-(((S)-1-amino-1-oxo-3-((S)-2-oxopyrrolidin-3-yl)propan-2-yl)amino)-3-cyclopropyl-1-oxopropan-2-yl)-4-methoxy-1H-indole-2-carboxamide(100 mg, crude) in DCM (4 mL) was added Burgess reagent (104.63 mg,439.07 umol, 2 eq). The mixture was stirred at 25° C. for 16 h. Thereaction mixture was quenched by water (0.5 mL) and was dried by blowingN₂. The residue was purified by neutral prep-HPLC to get the productN—((S)-1-(((S)-1-cyano-2-((S)-2-oxopyrrolidin-3-yl)ethyl)amino)-3-cyclopropyl-1-oxopropan-2-yl)-4-methoxy-1H-indole-2-carboxamide(15 mg, 34.29 umol, 15.62% yield, 100% purity) as a solid. MS (ESI) m/z438.2 [M+H]⁺.

prep-HPLC condition:

column: Waters Xbridge BEH C18 100*25 mm*5 um; mobile phase: [water (10mM NH₄HCO₃)-ACN]; B %: 20%-50%, 10 min.

¹H NMR (400 MHz, DMSO-d₆) δ ppm 11.57 (d, J=1.8 Hz, 1H), 8.90 (d, J=8.2Hz, 1H), 8.50 (d, J=7.5 Hz, 1H), 7.78-7.65 (m, 1H), 7.36 (d, J=1.5 Hz,1H), 7.13-7.04 (m, 1H), 7.03-6.96 (m, 1H), 6.50 (d, J=7.8 Hz, 1H),5.04-4.94 (m, 1H), 4.54-4.38 (m, 1H), 3.89 (s, 3H), 3.19-3.06 (m, 2H),2.44-2.33 (m, 1H), 2.22-2.07 (m, 2H), 1.90-1.75 (m, 2H), 1.74-1.63 (m,1H), 1.54-1.41 (m, 1H), 0.87-0.73 (m, 1H), 0.47-0.34 (m, 2H), 0.25-0.15(m, 1H), 0.14-0.04 (m, 1H).

Example 23. Synthesis of Viral Protease Inhibitor Compound 401

Step 1: (S)-methyl 2-amino-3-((S)-2-oxopyrrolidin-3-yl)propanoate

Methyl(2S)-2-(tert-butoxycarbonylamino)-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(400 mg, 1.40 mmol, 1 eq) in HCl/EtOAc (4 M, 10 mL, 28.63 eq) wasstirred at 25° C. for 0.5 h. Upon completion, the mixture wasconcentrated under the reduced pressure affording the product methyl(2S)-2-amino-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate (300 mg, crude,HCl) as a solid.

Step 2:(S)-tert-butyl3-(((S)-1-methoxy-1-oxo-3-((S)-2-oxopyrrolidin-3-yl)propan-2-yl)carbamoyl)-2-azaspiro[4.4]nonane-2-carboxylate

Methyl (2S)-2-amino-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate (300 mg,1.35 mmol, 1 eq, HCl) and(3S)-2-tertbutoxycarbonyl-2-azaspiro[4.4]nonane-3-carboxylic acid(362.87 mg, 1.35 mmol, 1 eq) in DMF (2 mL) and DCM (5 mL) was added DMAP(329.19 mg, 2.69 mmol, 2 eq) and EDCI (516.56 mg, 2.69 mmol, 2 eq). Themixture was stirred at 25° C. for 1 h. Upon completion, the reactionmixture was quenched by addition H₂O (10 mL), and then extracted withDCM (10 mL*3). The combined organic layers were washed with brine (10mL), dried over Na₂SO₄, filtered and concentrated under reduced pressureto give a residue. The residue was purified by column chromatography(SiO₂, petroleum ether:EtOAc=5:1 to 0:1) affording the producttert-butyl(3S)-3-[[(1S)-2-methoxy-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]carbamoyl]-2-azaspiro[4.4]nonane-2-carboxylate(340 mg, 777.09 umol, 57.68% yield) as an oil.

Step 3:(S)-methyl3-((S)-2-oxopyrrolidin-3-yl)-2-((S)-2-azaspiro[4.4]nonane-3-carboxamido)propanoate

tert-Butyl(3S)-3-[[(1S)-2-methoxy-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]carbamoyl]-2-azaspiro[4.4]nonane-2-carboxylate(340 mg, 777.09 umol, 1 eq) in HCl/EtOAc (4 M, 10 mL, 51.47 eq) wasstirred at 25° C. for 1 h. Upon completion, the mixture was concentratedunder the reduced pressured affording the productmethyl(2S)-2-[[(3S)-2-azaspiro[4.4]nonane-3-carbonyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(250 mg, crude, HCl) as an oil.

Step 4:(S)-methyl2-((S)-2-(4-methoxy-1H-indole-2-carbonyl)-2-azaspiro[4.4]nonane-3-carboxamido)-3-((S)-2-oxopyrrolidin-3-yl)propanoate

Methyl(2S)-2-[[(3S)-2-azaspiro[4.4]nonane-3-carbonyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(250 mg, 668.67 umol, 1 eq, HCl) and 4-methoxy-1H-indole-2-carboxylicacid (127.84 mg, 668.67 umol, 1 eq) in DMF (2 mL) and DCM (6 mL) wasadded DMAP (163.38 mg, 1.34 mmol, 2 eq) and EDCI (256.37 mg, 1.34 mmol,2 eq). The mixture was stirred at 25° C. for 2 h. Upon completion, thereaction mixture was quenched by addition H₂O (10 mL), and thenextracted with DCM (10 mL*3). The combined organic layers were washedwith brine (10 mL), dried over Na₂SO₄, filtered and concentrated underreduced pressure to give a residue. The residue was purified by prep-TLC(SiO₂, petroleum ether:EtOAc=0:1) affording the productmethyl(2S)-2-[[(3S)-2-(4-methoxy-1H-indole-2-carbonyl)-2-azaspiro[4.4]nonane-3-carbonyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(180 mg, 352.54 umol, 52.72% yield) as an oil. MS (ESI) m/z 511.2 [M+H]⁺

Step 5:(S)—N—((S)-1-amino-1-oxo-3-((S)-2-oxopyrrolidin-3-yl)propan-2-yl)-2-(4-methoxy-1H-indole-2-carbonyl)-2-azaspiro[4.4]nonane-3-carboxamide

Methyl(2S)-2-[[(3S)-2-(4-methoxy-1H-indole-2-carbonyl)-2-azaspiro[4.4]nonane-3-carbonyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(180 mg, 352.54 umol, 1 eq) in ammonia (7 M, 20 mL, 397.12 eq) wasstirred at 80° C. for 16 h. Upon completion, the mixture wasconcentrated under the reduced pressure affording the product(3S)—N-[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]-2-(4-methoxy-1H-indole-2-carbonyl)-2-azaspiro[4.4]nonane-3-carboxamide(170 mg, crude) as an oil.

Step 6:(S)—N—((S)-1-cyano-2-((S)-2-oxopyrrolidin-3-yl)ethyl)-2-(4-methoxy-1H-indole-2-carbonyl)-2-azaspiro[4.4]nonane-3-carboxamide

(3S)—N-[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]-2-(4-methoxy-1H-indole-2-carbonyl)-2-azaspiro[4.4]nonane-3-carboxamide(170 mg, 343.04 umol, 1 eq) in DCM (3 mL) was addedmethoxycarbonyl-(triethylammonio)sulfonyl-azanide (408.74 mg, 1.72 mmol,5 eq). The mixture was stirred at 25° C. for 1 h. Upon completion, themixture was concentrated under the reduced pressure to give a residue.The residue was purified by prep-HPLC (column: Waters Xbridge BEH C18100*25 mm*5 um; mobile phase: [water (10 mM NH₄HCO₃)-ACN]; B %: 30%-60%,10 min) affording the product(3S)—N-[(1S)-1-cyano-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]-2-(4-methoxy-1H-indole-2-carbonyl)-2-azaspiro[4.4]nonane-3-carboxamide(25 mg, 51.09 umol, 14.89% yield, 97.6% purity) as a solid. MS (ESI) m/z478.2 [M+H]⁺

¹H NMR (400 MHz, MMeOD-d₄) δ=7.22-7.12 (m, 1H), 7.11-6.98 (m, 2H),6.58-6.45 (m, 1H), 5.11-4.95 (m, 1H), 4.65-4.52 (m, 1H), 3.94 (s, 3H),3.93-3.80 (m, 2H), 3.28-3.18 (m, 1H), 2.54-2.02 (m, 4H), 2.01-1.48 (m,12H).

Example 24. Synthesis of Viral Protease Inhibitor Compound 225

Step 1: methyl (2S)-2-amino-3-(3-methylimidazol-4-yl)propanoate

To the solution of(2S)-2-(tert-butoxycarbonylamino)-3-(3-methylimidazol-4-yl)propanoicacid (300 mg, 1.11 mmol, 1 eq) in EtOAc (1.2 mL) was added HCl/EtOAc (4M, 2.79 mL, 10 eq) at 25° C. The reaction mixture was stirred at 25° C.for 1.5 h. The resulting mixture was concentrated to get the product.Methyl (2S)-2-amino-3-(3-methylimidazol-4-yl)propanoate (250 mg, crude,HCl) was obtained as a solid and used directly next step. MS (ESI) m/z183.2 [M+H]⁺

¹H NMR (400 MHz, METHANOL-d₄) δ ppm 8.94 (s, 1H), 7.56 (s, 1H), 4.51 (t,J=7.17 Hz, 1H), 3.93 (s, 3H), 3.87 (s, 3H), 3.46-3.55 (m, 1H), 3.32-3.42(m, 1H).

Step 2: methyl(2S)-2-[[(2S)-2-(tert-butoxycarbonylamino)-4-methyl-pentanoyl]amino]-3-(3-methylimidazol-4-yl)propanoate

To a mixture of methyl (2S)-2-amino-3-(3-methylimidazol-4-yl)propanoate(250 mg, 1.14 mmol, 1 eq, HCl) and(2S)-2-(tert-butoxycarbonylamino)-4-methyl-pentanoic acid (263.22 mg,1.14 mmol, 1 eq) in THF (1 mL) and DCM (1 mL) and DIPEA (441.26 mg, 3.41mmol, 594.69 uL, 3 eq) was added T3P (1.09 g, 1.71 mmol, 1.02 mL, 50%purity, 1.5 eq) at 0° C. under N₂. The mixture was stirred at 25° C. for10 h. LCMS showed the reaction mixture was completed. The reactionmixture was added saturated sodium bicarbonate solution (10 mL) andextracted with DCM (10 mL×2) to get the organic phase. The organic phasewas washed with brine (3 mL×3), dried over anhydrous sodium sulfate andconcentrated to get the crude product. Methyl(2S)-2-[[(2S)-2-(tert-butoxy carbonylamino)-4-methyl-pentanoyl]amino]-3-(3-methylimidazol-4-yl)propanoate(360 mg, crude) was obtained as an oil and used directly next step. MS(ESI) m/z 397.3 [M+H]⁺

Step 3:methyl(2S)-2-[[(2S)-2-amino-4-methyl-pentanoyl]amino]-3-(3-methylimidazol-4-yl)propanoate

To a mixture of methyl(2S)-2-[[(2S)-2-(tert-butoxycarbonylamino)-4-methyl-pentanoyl]amino]-3-(3-methylimidazol-4-yl)propanoate(360 mg, 907.99 umol, 1 eq) in DCM (3.3 mL) was added TFA (1.04 g, 9.08mmol, 672.27 uL, 10 eq) at 25° C. under N₂. The mixture was stirred at25° C. for 1.5 h. LCMS showed the reaction mixture was completed. Thereaction mixture was concentrated to get the product. Methyl(2S)-2-[[(2S)-2-amino-4-methyl-pentanoyl]amino]-3-(3-methylimidazol-4-yl)propanoate (370 mg, crude, TFA) was obtained as an oil and used directlynext step. MS (ESI) m/z 297.2 [M+H]⁺

Step 4: methyl(2S)-2-[[(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4-methyl-pentanoyl]amino]-3-(3-methylimidazol-4-yl)propanoate

To a mixture of methyl(2S)-2-[[(2S)-2-amino-4-methyl-pentanoyl]amino]-3-(3-methylimidazol-4-yl)propanoate(370 mg, 1.25 mmol, 1 eq, TFA) and 4-methoxy-1H-indole-2-carboxylic acid(238.69 mg, 1.25 mmol, 1 eq) in DMF (1.5 mL) and DCM (1.5 mL) was addedEDCI (478.66 mg, 2.50 mmol, 2 eq) and DMAP (305.05 mg, 2.50 mmol, 2 eq)in one portion at 25° C. under N₂. The mixture was stirred at 25° C. for12 h. The resulting mixture was added with water (10 mL) and extractedwith DCM (10 mL*2) to get the organic phase. The organic phase waswashed with brine (3 mL*3) and dried over anhydrous sodium sulfate andconcentrated to get the crude product. The residue was purified bycolumn chromatography (SiO2, petroleum ether/EtOAc=2/1 toEtOAc/Methanol=10/1). Methyl(2S)-2-[[(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4-methyl-pentanoyl]amino]-3-(3-methylimidazol-4-yl)propanoate(270 mg, crude) was obtained as an oil. MS (ESI) m/z 469.5 [M+H]⁺

Step 5:N-[(1S)-1-[[(1S)-2-amino-1-[(3-methylimidazol-4-yl)methyl]-2-oxo-ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide

To methyl(2S)-2-[[(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4-methyl-pentanoyl]amino]-3-(3-methylimidazol-4-yl)propanoate(235.00 mg, 500.50 umol, 1 eq) was added NH₃/MeOH (7 M, 1.94 mL, 27.14eq) in one portion at 25° C. under N₂. The mixture was stirred at 80° C.and stirred for 12 h. LCMS showed the reaction mixture was completed.The reaction mixture was cooled to 25° C. and concentrated to get thecrude product. The residue was purified by prep-TLC.N-[(1S)-1-[[(1S)-2-amino-1-[(3-methylimidazol-4-yl)methyl]-2-oxo-ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide(170 mg, crude) was obtained as a solid. MS (ESI) m/z 455.3 [M+H]⁺

Step 6:N-[(1S)-1-[[(1S)-1-cyano-2-(3-methylimidazol-4-yl)ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide

To a mixture ofN-[(1S)-1-[[(1S)-2-amino-1-[(3-methylimidazol-4-yl)methyl]-2-oxo-ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide(140 mg, 308.02 umol, 1 eq) in DCM (2 mL) was added Burgess reagent(293.61 mg, 1.23 mmol, 4 eq) at 25° C. under N₂. The mixture was stirredat 25° C. for 12 h, and then concentrated to get the crude product. Thecrude product was purified by pre-HPLC.N-[(1S)-1-[[(1S)-1-cyano-2-(3-methylimidazol-4-yl)ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide(10.59 mg, 23.82 umol, 7.73% yield, 98.2% purity) was obtained as asolid. MS (ESI) m/z 437.2 [M+H]⁺.

Prep-HPLC condition:

column: Phenomenex Gemini-NX C18 75*30 mm*3 um; mobile phase: [water (10mM NH₄HCO₃)-ACN]; B %: 25%-50%, 6 min

column: Waters Xbridge BEH C18 100*30 mm*10 um; mobile phase: [water (10mM NH₄HCO₃)-ACN]; B %: 20%-45%, 8 min

¹H NMR (400 MHz, METHANOL-d₄) δ ppm 7.52-7.57 (m, 1H), 7.28 (s, 1H),7.12-7.18 (m, 1H), 7.03 (d, J=8.38 Hz, 1H), 6.85-6.96 (m, 1H), 6.52 (d,J=7.72 Hz, 1H), 5.05-5.13 (m, 1H), 4.55-4.62 (m, 1H), 3.86-3.99 (m, 3H),3.68 (s, 3H), 3.21 (tt, J=15.24, 7.80 Hz, 2H), 1.55-1.81 (m, 3H),0.86-1.07 (m, 6H)

Example 25. Synthesis of Viral Protease Inhibitor Compound 227

Step 1: methyl (2S)-2-amino-3-(1-methylimidazol-4-yl)propanoate

To a mixture of (2S)-2-amino-3-(1-methylimidazol-4-yl)propanoic acid(0.5 g, 2.96 mmol, 1 eq) was added HCl/MeOH (4 M, 7.39 mL, 10 eq) in oneportion at 25° C. under N₂. The mixture was stirred at 25° C. for 2 h.The reaction mixture was concentrated to get the product. Methyl(2S)-2-amino-3-(1-methylimidazol-4-yl)propanoate (0.6 g, crude, HCl) wasobtained as a solid and used directly next step. MS (ESI) m/z 184.1[M+H]⁺

Step 2: methyl(2S)-2-[[(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4-methyl-pentanoyl]amino]-3-(1-methylimidazol-4-yl)propanoate

To a mixture of(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4-methyl-pentanoic acid(498.76 mg, 1.64 mmol, 1.2 eq) and methyl(2S)-2-amino-3-(1-methylimidazol-4-yl)propanoate (0.3 g, 1.37 mmol, 1eq, HCl), DIPEA (882.53 mg, 6.83 mmol, 1.19 mL, 5 eq) in THF (0.9 mL)and DCM (0.9 mL) was added T3P (1.30 g, 2.05 mmol, 1.22 mL, 50% purity,1.5 eq) at 0° C. under N₂. The mixture was stirred at 25° C. for 12 h.The reaction mixture was added to saturated sodium bicarbonate solution(10 mL) and extracted with DCM (10 mL*2) to get the organic phase. Theorganic phase was washed with brine (3 mL*3) and dried over anhydroussodium sulfate and concentrated to get the crude product. The residuewas purified by prep-HPLC. Methyl(2S)-2-[[(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4-methyl-pentanoyl]amino]-3-(1-methylimidazol-4-yl)propanoate(100 mg, 202.97 umol, 14.86% yield, 95.3% purity) was obtained as asolid. MS (ESI) m/z 470.2 [M+H]⁺

Prep-HPLC condition:

column: Kromasil C18 (250*50 mm*10 um); mobile phase: [water (10 mMNH₄HCO₃)-ACN]; B %: 25%-50%, 10 min

Step 3:N-[(1S)-1-[[(1S)-2-amino-1-[(1-methylimidazol-4-yl)methyl]-2-oxo-ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide

To methyl(2S)-2-[[(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4-methyl-pentanoyl]amino]-3-(1-methylimidazol-4-yl)propanoate(100 mg, 212.98 umol, 1 eq) was added NH₃/MeOH (7 M, 10.00 mL, 328.67eq) in one portion at 25° C. under N₂. The mixture was stirred at 80° C.for 12 h. The reaction mixture was cooled to 25° C. and concentrated toget the product.N-[(1S)-1-[[(1S)-2-amino-1-[(1-methylimidazol-4-yl)methyl]-2-oxo-ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide(95.5 mg, 190.57 umol, 89.48% yield, 90.7% purity) was obtained as asolid and used directly next step. MS (ESI) m/z 455.2 [M+H]⁺

Step 4: N-[(1S)-1-[[(1S)-1-cyano-2-(1-methylimidazol-4-yl)ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide

To a mixture ofN-[(1S)-1-[[(1S)-2-amino-1-[(1-methylimidazol-4-yl)methyl]-2-oxo-ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide(80.00 mg, 176.01 umol, 1 eq) in DCM (1 mL) was added Burgess reagent(83.89 mg, 352.02 umol, 2 eq) in one portion at 25° C. under N₂. Themixture was stirred at 25° C. for 12 h. The reaction mixture was addedthe water (0.3 mL) and stirred for 10 min. Then the reaction mixture wasconcentrated to get the crude product. The crude product was purified byprep-HPLC. N-[(1S)-1-[[(1S)-1-cyano-2-(1-methylimidazol-4-yl)ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide (26.39 mg,60.27 umol, 34.24% yield, 99.684% purity) was obtained as a solid. MS(ESI) m/z 437.2 [M+H]⁺

Prep-HPLC condition:

column: Waters Xbridge BEH C18 100*25 mm*5 um; mobile phase: [water (10mM NH₄HCO₃)-ACN]; B %: 25%-55%, 10 min

¹H NMR (400 MHz, METHANOL-d₄) δ ppm 7.35 (s, 1H), 7.28 (s, 1H),7.12-7.20 (m, 1H), 7.05 (d, J=8.38 Hz, 1H), 6.91-6.98 (m, 1H), 6.53 (d,J=7.72 Hz, 1H), 5.01 (t, J=7.06 Hz, 1H), 4.63 (br dd, J=9.59, 4.96 Hz,1H), 3.94 (s, 3H), 3.46-3.59 (m, 3H), 3.00-3.13 (m, 2H), 1.61-1.81 (m,3H), 0.89-1.07 (m, 6H)

Step 5: tert-butyl(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4-methyl-pentanoate

To a mixture of 4-methoxy-1H-indole-2-carboxylic acid (5 g, 26.15 mmol,1 eq) and tert-butyl (2S)-2-amino-4-methyl-pentanoate (5.88 g, 31.38mmol, 1.2 eq, HCl), EDCI (6.52 g, 34.00 mmol, 1.3 eq), HOBt (4.59 g,34.00 mmol, 1.3 eq) in DMF (30 mL) was added TEA (7.94 g, 78.46 mmol,10.92 mL, 3 eq) in one portion at 25° C. under N₂. The mixture wasstirred at 25° C. and stirred for 2 h. The reaction mixture was addedwater (90 mL) and extracted with EtOAc (25 mL*3) to get the organicphase. The organic phase was washed with 5% citric acid (25 mL) and 5%aqueous solution of sodium bicarbonate (25 mL) and dried over anhydroussodium sulfate, filtered and concentrated to get the product. Theresidue was purified by column chromatography (SiO₂, petroleumether:EtOAc=30:1 to 10:1). Tert-butyl(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4-methyl-pentanoate (5.93g, 16.45 mmol, 62.91% yield) was obtained as solid. MS (ESI) m/z 361.2[M+H]⁺

¹H NMR (400 MHz, CHLOROFORM-d) δ ppm 9.25 (br s, 1H), 7.10-7.16 (m, 1H),6.93-7.00 (m, 2H), 6.56 (br d, J=8.31 Hz, 1H), 6.44 (d, J=7.70 Hz, 1H),4.66 (td, J=8.50, 5.14 Hz, 1H), 3.88 (s, 3H), 1.62-1.75 (m, 2H),1.57-1.62 (m, 1H), 1.42 (s, 9H), 0.92 (dd, J=6.17, 3.85 Hz, 6H).

Step 6:(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4-methyl-pentanoic acid

To a mixture of tert-butyl(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4-methyl-pentanoate (2.00g, 5.55 mmol, 1 eq) in DCM (8 mL) was added TFA (10.27 g, 90.04 mmol,6.67 mL, 16.23 eq) and H₂O (666.67 mg, 37.01 mmol, 666.67 uL, 6.67 eq)in one portion at 0° C. under N₂. The mixture was stirred at 25° C. andstirred for 4 h. The reaction mixture was concentrated to get the crudeproduct.(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4-methyl-pentanoic acid(2.24 g, 5.35 mmol, 96.50% yield, TFA) was obtained as a solid and useddirectly next step. MS (ESI) m/z 305.1 [M+H]⁺

Example 26. Synthesis of Viral Protease Inhibitor Compound 231

Step 1: (S)-methyl 2-amino-3-(pyridin-3-yl)propanoate hydrochloride

To a mixture of (2S)-2-(tert-butoxycarbonylamino)-3-(3-pyridyl)propanoicacid (500 mg, 1.88 mmol, 1 eq) was added HCl/MeOH (4 M, 20.80 mL, 44.31eq) in one portion at 25° C. under N₂. The mixture was stirred at 25° C.and stirred for 12 h. Upon completion, the reaction mixture wasconcentrated to get methyl (2S)-2-amino-3-(3-pyridyl)propanoate (400 mg,crude, HCl) as an oil and used directly for the next step. MS (ESI) m/z181.1 [M+H]⁺

Step 2: (S)-methyl2-((S)-2-(4-methoxy-1H-indole-2-carboxamido)-4-methylpentanamido)-3-(pyridine-3-yl)propanoate

To a mixture of methyl (2S)-2-amino-3-(3-pyridyl)propanoate (0.3 g, 1.66mmol, 1 eq, HCl) and(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4-methyl-pentanoic acid(506.66 mg, 1.66 mmol, 1 eq), DIPEA (1.08 g, 8.32 mmol, 1.45 mL, 5 eq)in THF (0.6 mL) and DCM (0.6 mL) was added T3P (1.59 g, 2.50 mmol, 1.49mL, 50% purity, 1.5 eq) at 0° C. under N₂. The mixture was stirred at25° C. for 12 h. Upon completion, the reaction mixture was addedsaturated sodium bicarbonate solution (10 mL) and extracted with DCM (10mL*2) to get the organic phase. The organic phase was concentrated toget the crude product. The residue was purified by pulping withpetroleum ether (20 mL) and filtered to get the filter cake as theproduct. Methyl(2S)-2-[[(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4-methyl-pentanoyl]amino]-3-(3-pyridyl)propanoate(0.4 g, crude) was obtained as a solid and used directly next step. MS(ESI) m/z 467.1 [M+H]⁺

Step 3:N—((S)-1-(((S)-1-amino-1-oxo-3-(pyridin-3-yl)propan-2-yl)amino)-4-methyl-1-oxopentan-2-yl)-4-methoxy-1H-indole-2-carboxamide

To a mixture of methyl(2S)-2-[[(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4-methyl-pentanoyl]amino]-3-(3-pyridyl)propanoate(200.00 mg, 428.70 umol, 1 eq) was added NH₃/MeOH (7 M, 5 mL, 81.64 eq)in one portion at 25° C. under N₂. The mixture was stirred at 80° C. for4 h. Upon completion, the reaction mixture was cooled to 25° C. andconcentrated to getN-[(1S)-1-[[(1S)-2-amino-2-oxo-1-(3-pyridylmethyl)ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide(0.18 g, 339.65 umol, 79.23% yield, 85.2% purity) as a solid and useddirectly next step. MS (ESI) m/z 452.2 [M+H]⁺

Step 3:N—((S)-1-(((S)-1-cyano-2-(pyridin-3-yl)ethyl)amino)-4-methyl-1-oxopentan-2-yl)-4-methoxy-1H-indole-2-carboxamide

To a mixture ofN-[(1S)-1-[[(1S)-2-amino-2-oxo-1-(3-pyridylmethyl)ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide(0.1 g, 221.48 umol, 1 eq) in DCM (1 mL) was added Burgess reagent(105.56 mg, 442.95 umol, 2 eq) in one portion at 25° C. under N₂. Themixture was stirred at 25° C. for 12 h. The Burgess reagent (105.56 mg,442.95 umol, 2 eq) was re-added into the above solution at 25° C. andthe reaction mixture was stirred at 25° C. for 1 h. Upon completion, thereaction mixture was added the water (0.5 mL) and stirred for 10 min.Then the mixture was concentrated to get the crude product. The crudeproduct was purified by pre-HPLC to giveN-[(1S)-1-[[(1S)-1-cyano-2-(3-pyridyl)ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide(23.18 mg, 52.94 umol, 23.90% yield, 99.009% purity) as a solid. MS(ESI) m/z 434.2 [M+H]⁺

Prep-HPLC condition:

column: Waters Xbridge BEH C18 100*25 mm*5 um; mobile phase: [water (10mM NH₄HCO₃)-ACN]; B %: 30%-60%, 10 min

¹H NMR (400 MHz, METHANOL-d₄) δ ppm 8.47-8.52 (m, 1H), 8.34-8.45 (m,1H), 7.77-7.84 (m, 1H), 7.28-7.38 (m, 1H), 7.23-7.28 (m, 1H), 7.12-7.19(m, 1H), 6.99-7.07 (m, 1H), 6.52 (d, J=7.63 Hz, 1H), 5.08-5.18 (m, 1H),4.48-4.61 (m, 1H), 3.94 (s, 3H), 3.12-3.29 (m, 2H), 1.41-1.76 (m, 3H),0.87-1.03 (m, 6H).

Step 5: (S)-tert-butyl2-(4-methoxy-1H-indole-2-carboxamido)-4-methylpentanoate

To a mixture of 4-methoxy-1H-indole-2-carboxylic acid (5 g, 26.15 mmol,1 eq) and tert-butyl (2S)-2-amino-4-methyl-pentanoate (5.88 g, 31.38mmol, 1.2 eq, HCl), EDCI (6.52 g, 34.00 mmol, 1.3 eq), HOBt (4.59 g,34.00 mmol, 1.3 eq) in DMF (30 mL) was added TEA (7.94 g, 78.46 mmol,10.92 mL, 3 eq) in one portion at 25° C. under N₂. The mixture wasstirred at 25° C. and stirred for 2 h. Upon completion, the reactionmixture was added water (90 mL) and extracted with ethyl acetate (25mL*3) to get the organic phase. The organic phase was washed with 5%citric acid (25 mL) and 5% aqueous solution of sodium bicarbonate (25mL) and dried over anhydrous sodium sulfate, filtered and concentratedto get the crude product. The residue was purified by columnchromatography (SiO₂, petroleum ether:EtOAc=30:1 to 10:1) to givetert-butyl(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4-methyl-pentanoate (5.93g, 16.45 mmol, 62.91% yield) as a solid. MS (ESI) m/z 361.2 [M+H]⁺

¹H NMR (400 MHz, CHLOROFORM-d) δ ppm 9.25 (br s, 1H), 7.10-7.16 (m, 1H),6.93-7.00 (m, 2H), 6.56 (br d, J=8.31 Hz, 1H), 6.44 (d, J=7.70 Hz, 1H),4.66 (td, J=8.50, 5.14 Hz, 1H), 3.88 (s, 3H), 1.62-1.75 (m, 2H),1.57-1.62 (m, 1H), 1.42 (s, 9H), 0.92 (dd, J=6.17, 3.85 Hz, 6H).

Step 6: (S)-2-(4-methoxy-1H-indole-2-carboxamido)-4-methylpentanoic acid

To a mixture of tert-butyl(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4-methyl-pentanoate (0.5g, 1.39 mmol, 1 eq) in DCM (0.33 mL) was added TFA (2.57 g, 22.51 mmol,1.67 mL, 16.23 eq) and H₂O (166.71 mg, 9.25 mmol, 166.71 uL, 6.67 eq) inone portion at 0° C. under N₂. The mixture was stirred at 25° C. andstirred for 2 h. Upon completion, the reaction mixture was concentratedto give (S)-2-(4-methoxy-1H-indole-2-carboxamido)-4-methylpentanoic acid(400 mg, crude, TFA) as a solid and used directly next step. MS (ESI)m/z 305.1 [M+H]⁺

Example 27. Synthesis of Viral Protease Inhibitor Compound 599

Step 1: tert-butyl(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)aminol-4-methyl-pentanoate

To a mixture of 4-methoxy-1H-indole-2-carboxylic acid (5 g, 26.15 mmol,1 eq) and tert-butyl (2S)-2-amino-4-methyl-pentanoate (5.88 g, 31.38mmol, 1.2 eq. HCl), EDCI (6.52 g, 34.00 mmol, 1.3 eq), HOBt (4.59 g,34.00 mmol, 1.3 eq) in DMF (30 ML) was added TEA (7.94 g, 78.46 mmol,10.92 mL, 3 eq) in one portion at 25° C. under N₂. The mixture wasstirred at 25° C. and stirred for 2 h. The reaction mixture was addedwith water (90 mL) and extracted with EtOAc (25 mL*3) to get the organicphase. The organic phase was washed with 5% citric acid (25 mL) and 5%aqueous solution of sodium bicarbonate (25 mL) and dried over anhydroussodium sulfate, filtered and concentrated to get the product. Theresidue was purified by column chromatography (SiO₂, petroleumether:EtOAc=30:1 to 10:1). Tert-butyl(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4-methyl-pentanoate (5.93g, 16.45 mmol, 62.91% yield) was obtained as a solid. MS (ESI) m/z 361.2[M+H].

¹H NMR (400 MHz, CHLOROFORM-d) δ ppm 9.25 (br s, 1H), 7.10-7.16 (m, 1H),6.93-7.00 (m, 2H), 6.56 (br d, J=8.31 Hz, 1H), 6.44 (d, J=7.70 Hz, 1H),4.66 (td, J=8.50, 5.14 Hz, 1H), 3.88 (s, 3H), 1.62-1.75 (m, 2H),1.57-1.62 (m, 1H), 1.42 (s, 9H), 0.92 (dd, J=6.17, 3.85 Hz, 6H).

Step 2:(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)aminol-4-methyl-pentanoic acid

To a mixture of tert-butyl(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4-methyl-pentanoate (2.00g, 5.55 mmol, 1 eq) in DCM (8 ML) was added TFA (10.27 g, 90.04 mmol,6.67 mL, 16.23 eq) and H₂O (666.67 mg, 37.01 mmol, 666.67 uL, 6.67 eq)in one portion at 0° C. under N₂. The mixture was stirred at 25° C. andstirred for 4 h. The reaction mixture was concentrated to get the crudeproduct.(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4-methyl-pentanoic acid(2.24 g, 5.35 mmol, 96.50% yield, TFA) was obtained as a solid and useddirectly next step. MS (ESI) m/z 305.1 [M+H]⁺

Step 3: methyl2-[[(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4-methyl-pentanoyl]amino]-3-(2-oxo-1H-quinolin-4-yl)propanoate

To a mixture of(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4-methyl-pentanoic acid(568.23 mg, 1.36 mmol, 1.2 eq, TFA) and methyl2-amino-3-(2-oxo-1H-quinolin-4-yl)propanoate (320 mg, 1.13 mmol, 1 eq,HCl), DIPEA (731.40 mg, 5.66 mmol, 985.72 uL, 5 eq) in THF (1 mL) andDCM (1 mL) was added T3P (1.08 g, 1.70 mmol, 1.01 mL, 50% purity, 1.5eq) at 0° C. under N₂. The mixture was stirred at 25° C. for 12 h. Thereaction mixture was added with saturated sodium bicarbonate solution(10 mL) and extracted with DCM (10 mL*2) to get the organic phase. Theorganic phase was concentrated to get the crude product. The residue waspurified by prep-HPLC. Methyl2-[[(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4-methyl-pentanoyl]amino]-3-(2-oxo-1H-quinolin-4-yl)propanoate(0.2 g, 375.53 umol, 33.18% yield) was obtained as a solid. MS (ESI) m/z533.2 [M+H]⁺

Prep-HPLC condition:

column: Kromasil C18 (250*50 mm*10 um); mobile phase: [water (10 mMNH₄HCO₃)-ACN]; B %: 30%-60%, 10 min

Step 4:N-[(1S)-1-[[2-amino-2-oxo-]-[(2-oxo-1H-quinolin-4-yl)methyl]ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide

To a mixture of methyl2-[[(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4-methyl-pentanoyl]amino]-3-(2-oxo-1H-quinolin-4-yl)propanoate (200.00 mg, 375.53 umol, 1eq) was added NH₃/MeOH (7 M, 10.00 mL, 186.41 eq) in one portion at 25°C. under N₂. The mixture was stirred at 80° C. for 12 h. The reactionmixture was cooled to 25° C. and concentrated to get the product.N-[(1S)-1-[[2-amino-2-oxo-1-[(2-oxo-1H-quinolin-4-yl)methyl]ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide(180 mg, 326.21 umol, 86.87% yield, 93.8% purity) was obtained as asolid and used directly next step. MS (ESI) m/z 518.2 [M+H]⁺

Step 5:N-[(1S)-1-[[-cyano-2-(2-oxo-H-quinolin-4-yl)ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide

To a mixture ofN-[(1S)-1-[[2-amino-2-oxo-1-[(2-oxo-1H-quinolin-4-yl)methyl]ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide(90 mg, 173.89 umol, 1 eq) in DCM (5 mL) was added Burgess reagent(207.19 mg, 869.44 umol, 5 eq) in one portion at 25° C. under N₂. Themixture was stirred at 25° C. for 12 h, and then concentrated to get thecrude product.

The residue was purified by prep-HPLC.N-[(1S)-1-[[1-cyano-2-(2-oxo-1H-quinolin-4-yl)ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide (20.74 mg,41.13 umol, 23.66% yield, 99.079% purity) was obtained as a solid. MS(ESI) m/z 500.2 [M+H]⁺

Prep-HPLC condition:

column: Waters Xbridge BEH C18 100*25 mm*5 um; mobile phase: [water (10mM NH₄HCO₃)-ACN]; B %: 30%-65%, 10 min

¹H NMR (400 MHz, METHANOL-d₄) δ ppm 7.93 (br d, J=8.16 Hz, 1H),7.50-7.58 (m, 1H), 7.28-7.40 (m, 2H), 7.26 (dd, J=11.47, 0.66 Hz, 1H),7.11-7.19 (m, 1H), 7.04 (dd, J=8.27, 4.08 Hz, 1H), 6.59-6.70 (m, 1H),6.46-6.56 (m, 1H), 5.24-5.34 (m, 1H), 4.53 (td, J=10.31, 5.18 Hz, 1H),3.93 (d, J=4.41 Hz, 3H), 3.40-3.59 (m, 3H), 1.72 (ddd, J=15.16, 9.87,5.18 Hz, 1H), 1.53-1.66 (m, 2H), 1.40-1.50 (m, 1H), 0.87-1.01 (m, 5H)

Step 6: methyl 2-amino-3-(2-oxo-1H-quinolin-4-yl)propanoate

To 2-amino-3-(2-oxo-1H-quinolin-4-yl)propanoic acid (400 mg, 1.72 mmol,1 eq) was added HCl/MeOH (4 M, 4.31 mL, 10 eq) in one portion at 25° C.under N₂. The mixture was stirred at 25° C. and stirred for 1 h. Thereaction mixture was concentrated to get the product. Methyl2-amino-3-(2-oxo-1H-quinolin-4-yl)propanoate (370 mg, crude, HCl) wasobtained as a solid and used directly next step.

Example 28. Synthesis of Viral Protease Inhibitor Compound 249

Step 1: 2-amino-3-(2-oxo-3,4-dihydro-1H-quinolin-4-yl)propanoic acid

To a solution of 2-amino-3-(2-oxo-1H-quinolin-4-yl)propanoic acid (200mg, 861.20 umol, 1 eq) in H₂O (1 mL) was added Pd/C (20 mg, 861.20 umol,10% purity) at 25° C. under N₂. The suspension was degassed under vacuumand purged with H₂ several times. The mixture was stirred under H₂(861.20 umol) (15 psi) at 70° C. for 5 h. The reaction mixture wascooled to 25° C. and filtered to get the filtrate. The filtrate wasconcentrated to get the product.2-amino-3-(2-oxo-3,4-dihydro-1H-quinolin-4-yl)propanoic acid (200 mg,crude) was obtained as a solid and used directly next step. MS (ESI) m/z235.0 [M+H]⁺

¹H NMR (400 MHz, METHANOL-d₄) δ ppm 1.92-2.03 (m, 1H) 2.06-2.21 (m, 1H)2.45-2.62 (m, 1H) 2.86 (dd, J=16.43, 6.06 Hz, 1H) 3.32-3.40 (m, 1H) 3.83(br dd, J=8.49, 5.84 Hz, 1H) 3.93 (br t, J=6.95 Hz, 1H) 6.93 (d, J=7.72Hz, 1H) 7.01-7.10 (m, 1H) 7.24 (br t, J=7.72 Hz, 1H) 7.36 (d, J=7.06 Hz,1H)

Step 2: methyl 2-amino-3-(2-oxo-3,4-dihydro-1H-quinolin-4-yl)propanoate

To 2-amino-3-(2-oxo-3,4-dihydro-1H-quinolin-4-yl)propanoic acid (200 mg,853.79 umol, 1 eq) was added HCl/MeOH (4 M, 9.91 mL, 46.45 eq) in oneportion at 25° C. under N₂. The mixture was stirred at 25° C. for 12 h.The reaction mixture was concentrated to get the crude product. Methyl2-amino-3-(2-oxo-3,4-dihydro-1H-quinolin-4-yl)propanoate (260 mg, crude,HCl) was obtained as the yellow oil and used directly next step. MS(ESI) m/z 249.1 [M+H]⁺

Step 3: methyl2-[[(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4-methyl-pentanoyl]amino]-3-(2-oxo-3,4-dihydro-1H-quinolin-4-yl)propanoate

To a mixture of methyl2-amino-3-(2-oxo-3,4-dihydro-1H-quinolin-4-yl)propanoate (260 mg, 913.12umol, 1 eq, HCl) and(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4-methyl-pentanoic acid(277.90 mg, 913.12 umol, 1 eq), DIPEA (590.07 mg, 4.57 mmol, 795.24 uL,5 eq) in THF (0.6 mL) and DCM (0.6 mL) was added T3P (871.61 mg, 1.37mmol, 814.59 uL, 50% purity, 1.5 eq) at 0° C. under N₂. The mixture wasstirred at 25° C. for 12 h. The reaction mixture was added saturatedsodium bicarbonate solution (10 mL) and extracted with DCM (10 mL*2) toget the organic phase. The organic phase was concentrated to get thecrude product. The residue was purified by pre-HPLC. Methyl2-[[(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4-methyl-pentanoyl]amino]-3-(2-oxo-3,4-dihydro-1H-quinolin-4-yl)propanoate(85 mg, 151.05 umol, 16.54% yield, 95% purity) was obtained as a solid.MS (ESI) m/z 535.2 [M+H]⁺

Prep-HPLC condition:

column: Phenomenex Gemini-NX 80*40 mm*3 um; mobile phase: [water (10 mMNH4HCO3)-ACN]; B %: 27%-47%, 8 min

Step 4:N-[(1S)-1-[[2-amino-2-oxo-1-[(2-oxo-3,4-dihydro-1H-quinolin-4-yl)methyl]ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide

To a mixture of methyl2-[[(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4-methyl-pentanoyl]amino]-3-(2-oxo-3,4-dihydro-1H-quinolin-4-yl)propanoate (55 mg, 102.88umol, 1 eq) was added NH₃/MeOH (7 M, 1.83 mL, 124.74 eq) in one portionat 25° C. under N₂. The mixture was stirred at 80° C. for 12 h. Thereaction mixture was cooled to the 25° C. and concentrated to get theproduct.N-[(1S)-1-[[2-amino-2-oxo-1-[(2-oxo-3,4-dihydro-1H-quinolin-4-yl)methyl]ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide(55 mg, crude) was obtained as a solid and used directly next step. MS(ESI) m/z 518.2 [M+H]⁺

Step 5:N-[(1S)-1-[[-cyano-2-(2-oxo-1H-quinolin-4-yl)ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide

To a mixture ofN-[(1S)-1-[[2-amino-2-oxo-1-[(2-oxo-3,4-dihydro-1H-quinolin-4-yl)methyl]ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide (75 mg,144.34 umol, 1 eq) in DCM (0.1 mL) was added Burgess reagent (103.19 mg,433.03 umol, 3 eq) in one portion at 25° C. under N₂. The mixture wasstirred at 25° C. and stirred for 16 h. The reaction mixture was addedwith water (0.5 mL) and stirred for 10 min. Then the mixture wasconcentrated to get the crude product. The crude product was purified bypre-HPLC. N-[(1S)-1-[[1-cyano-2-(2-oxo-3,4-dihydro-1H-quinolin-4-yl)ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide(26.51 mg, 52.85 umol, 36.62% yield, 100% purity) was obtained as asolid. MS (ESI) m/z 502.2 [M+H]⁺

Prep-HPLC condition:

column: Waters Xbridge BEH C18 100*25 mm*5 um; mobile phase: [water (10mM NH4HCO3)-ACN]; B %: 30%-60%, 10 min

¹H NMR (400 MHz, DMSO-d₆) δ ppm 11.51-11.61 (m, 1H), 10.14-10.20 (m,1H), 8.84-9.01 (m, 1H), 8.42-8.59 (m, 1H), 7.32-7.42 (m, 1H), 7.05-7.22(m, 3H), 6.81-7.04 (m, 3H), 6.50 (dd, J=7.64, 3.85 Hz, 1H), 4.37-4.66(m, 2H), 3.83-3.95 (m, 3H), 2.95-3.12 (m, 1H), 2.63-2.82 (m, 1H),2.26-2.42 (m, 1H), 1.88-2.08 (m, 2H), 1.45-1.82 (m, 3H), 0.81-1.02 (m,6H)

Step 6: (S)-tert-butyl2-(4-methoxy-1H-indole-2-carboxamido)-4-methylpentanoate

To a mixture of 4-methoxy-1H-indole-2-carboxylic acid (15 g, 78.46 mmol,1 eq) and tert-butyl (2S)-2-amino-4-methyl-pentanoate (21.07 g, 94.15mmol, 1.2 eq, HCl) in DMF (150 mL) was added EDCI (19.55 g, 102.00 mmol,1.3 eq), HOBt (13.78 g, 102.00 mmol, 1.3 eq), TEA (23.82 g, 235.38 mmol,32.76 mL, 3 eq) at 25° C. under N₂. The mixture was stirred at 25° C.and stirred for 2 h. The reaction mixture was added water (450 mL) andextracted with EtOAc (250 mL*3) to get the organic phase. The organicphase was washed with 5% citric acid (300 mL) and 5% aqueous solution ofsodium bicarbonate (300 mL) and dried over anhydrous sodium sulfate,filtered and concentrated to get the product. The residue was purifiedby column chromatography (SiO₂, petroleum ether:EtOAc=30:1 to 10:1).tert-butyl(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4-methyl-pentanoate (24g, 66.58 mmol, 84.87% yield) was obtained as a solid. MS (ESI) m/z 361.2[M+H]⁺

Step 7: (S)-2-(4-methoxy-1H-indole-2-carboxamido)-4-methylpentanoic acid

To a mixture of tert-butyl(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4-methyl-pentanoate (10g, 27.74 mmol, 1 eq) in DCM (30 mL) was added TFA (61.60 g, 540.26 mmol,40 mL, 19.47 eq) and H₂O (4.00 g, 221.98 mmol, 4.00 mL, 8.00 eq) in oneportion at 0° C. under N₂. The mixture was stirred at 25° C. for 2 h.The reaction mixture was concentrated to get the crude product. Thecrude product was purified with petroleum ether:ethyl acetate=10:1 (20mL) and filtered to get the product.(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4-methyl-pentanoic acid(6 g, 19.22 mmol, 69.27% yield, 97.48% purity) was obtained as a solid.MS (ESI) m/z 305.1 [M+H]⁺

Example 29. Synthesis of Viral Protease Inhibitor Compound 600

Step 1: methyl 2-amino-3-(2-oxo-1,2-dihydropyridin-3-yl)propanoate

A mixture of 2-amino-3-(2-oxo-1H-pyridin-3-yl)propanoic acid (500 mg,2.74 mmol, 1 eq) and HCl/MeOH (4 M, 30 mL, 43.72 eq) was stirred at 25°C. for 2 h. The reaction mixture was concentrated under reduced pressureto give a product methyl2-amino-3-(2-oxo-1,2-dihydropyridin-3-yl)propanoate (650 mg, crude, HCl)as a yellow oil and used directly for next step. MS (ESI) m/z 197.0[M+H]⁺

Step 2:methyl-2-((S)-2-((tert-butoxycarbonyl)amino)-4-methylpentanamido)-3-(2-oxo-1,2-dihydropyridin-3-yl)propanoate

A mixture of methyl 2-amino-3-(2-oxo-1H-pyridin-3-yl)propanoate (650 mg,2.79 mmol, 1 eq, HCl),(2S)-2-(tert-butoxycarbonylamino)-4-methyl-pentanoic acid (646.16 mg,2.79 mmol, 1 eq), EDCI (1.07 g, 5.59 mmol, 2 eq), DMAP (682.62 mg, 5.59mmol, 2 eq), DMF (2 mL) and DCM (4 mL) was stirred at 25° C. for 1 h.The reaction mixture was diluted with H₂O (30 mL) and extracted with DCM(30 mL*3). The combined organic layers were washed with brine (50 mL),dried over Na₂SO₄, filtered and concentrated under reduced pressure togive a residue. The residue was purified by column chromatography (SiO₂,petroleum ether/EtOAc=0/1) to get the productmethyl-2-((S)-2-((tert-butoxycarbonyl)amino)-4-methylpentanamido)-3-(2-oxo-1,2-dihydropyridin-3-yl)propanoate(900 mg, 1.89 mmol, 67.68% yield, 86.02% purity), as a solid. MS (ESI)m/z 410.1 [M+H]⁺

Step 3: methyl2-((S)-2-amino-4-methylpentanamido)-3-(2-oxo-1,2-dihydropyridin-3-yl)propanoate

A mixture ofmethyl-2-((S)-2-((tert-butoxycarbonyl)amino)-4-methylpentanamido)-3-(2-oxo-1,2-dihydropyridin-3-yl)propanoate(200 mg, 488.43 umol, 1 eq) and HCl/EtOAc (4 M, 30 mL) was stirred at27° C. for 0.5 h. The reaction mixture was concentrated under reducedpressure to give a product methyl2-((S)-2-amino-4-methylpentanamido)-3-(2-oxo-1,2-dihydropyridin-3-yl)propanoate(170 mg, crude, HCl) as a solid and used directly for next step.

Step 4: methyl2-((S)-2-(4-methoxy-1H-indole-2-carboxamido)-4-methylpentanamido)-3-(2-oxo-1,2-dihydropyridin-3-yl)propanoate

A mixture of methyl2-((S)-2-amino-4-methylpentanamido)-3-(2-oxo-1,2-dihydropyridin-3-yl)propanoate(170 mg, 491.58 umol, 1 eq, HCl), 4-methoxy-1H-indole-2-carboxylic acid(93.98 mg, 491.58 umol, 1 eq), EDCI (188.47 mg, 983.17 umol, 2 eq), DMAP(120.11 mg, 983.17 umol, 2 eq), DMF (2 mL) and DCM (4 mL) was stirred at25° C. for 1 h. The reaction mixture was diluted with H₂O (30 mL) andthen extracted with DCM (30 mL*3). The combined organic layers werewashed with brine (50 mL), dried over Na₂SO₄, filtered and concentratedunder reduced pressure to give a residue. The residue was purified bycolumn chromatography (SiO₂, petroleum ether/EtOAc=0/1) to get thecompound methyl2-((S)-2-(4-methoxy-1H-indole-2-carboxamido)-4-methylpentanamido)-3-(2-oxo-1,2-dihydropyridin-3-yl)propanoate(130 mg, 269.41 umol, 54.81% yield), as a solid. MS (ESI) m/z 483.1[M+H]⁺

Step 5:N-((2S)-1-((1-amino-1-oxo-3-(2-oxo-1,2-dihydropyridin-3-yl)propan-2-yl)amino)-4-methyl-1-oxopentan-2-yl)-4-methoxy-1H-indole-2-carboxamide

A mixture of methyl2-((S)-2-(4-methoxy-1H-indole-2-carboxamido)-4-methylpentanamido)-3-(2-oxo-1,2-dihydropyridin-3-yl)propanoate(190 mg, 393.76 umol, 1 eq), NH₃/MeOH (7 M, 10 mL) was stirred at 80° C.for 15 h. The reaction mixture was concentrated under reduced pressureto giveN-((2S)-1-((1-amino-1-oxo-3-(2-oxo-1,2-dihydropyridin-3-yl)propan-2-yl)amino)-4-methyl-1-oxopentan-2-yl)-4-methoxy-1H-indole-2-carboxamide(190 mg, crude) as a solid. MS (ESI) m/z 468.2 [M+H]⁺

Step 6:N-((2S)-1-((1-cyano-2-(2-oxo-1,2-dihydropyridin-3-yl)ethyl)amino)-4-methyl-1-oxopentan-2-yl)-4-methoxy-1H-indole-2-carboxamide

A mixture ofN-((2S)-1-((1-amino-1-oxo-3-(2-oxo-1,2-dihydropyridin-3-yl)propan-2-yl)amino)-4-methyl-1-oxopentan-2-yl)-4-methoxy-1H-indole-2-carboxamide(180 mg, 385.01 umol, 1 eq), Burgess reagent (917.53 mg, 3.85 mmol, 10eq) and DCM (30 mL) was stirred at 25° C. for 8 h. The reaction mixturewas concentrated under reduced pressure to give a residue. The residuewas purified by prep-HPLC (column: Phenomenex Gemini-NX C18 75*30 mm*3um; mobile phase: [water (0.05% NH₃H₂O+10 mM NH₄HCO₃)-ACN]; B %:25%-45%, 8 min) to get the productN-((2S)-1-((1-cyano-2-(2-oxo-1,2-dihydropyridin-3-yl)ethyl)amino)-4-methyl-1-oxopentan-2-yl)-4-methoxy-1H-indole-2-carboxamide(24 mg, 52.18 umol, 13.55% yield, 97.73% purity), as a solid. MS (ESI)m/z 450.2 [M+H]⁺.

¹H NMR (400 MHz, DMSO-d₆) δ=11.90-11.40 (m, 2H), 9.08-8.85 (m, 1H),8.55-8.35 (m, 1H), 7.51-7.26 (m, 3H), 7.16-7.05 (m, 1H), 7.04-6.94 (m,1H), 6.51 (d, J=7.5 Hz, 1H), 6.15 (t, J=6.6 Hz, 1H), 5.19-5.01 (m, 1H),4.55-4.33 (m, 1H), 3.89 (s, 3H), 3.02-2.78 (m, 2H), 1.75-1.33 (m, 3H),0.98-0.72 (m, 6H)

Example 30. Synthesis of Viral Protease Inhibitor Compounds 344C, 344D,507 and 511

Step for Compound 344C.N-[(1S)-1-[[(1S)-2-amino-2-cyano-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide

To a mixture ofN-[(1S)-1-[[(1S)-1-formyl-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide(100 mg, 180.79 umol, 80% purity, 1 eq) in DCM (10 mL) was added NH₃.H₂O(46.93 mg, 361.58 umol, 51.57 uL, 27% purity, 2 eq) and NH₄Cl (19.34 mg,361.58 umol, 2 eq). The mixture was stirred at 25° C. for 30 min, thenadded KCN (94.18 mg, 1.45 mmol, 61.96 uL) in H₂O (0.2 mL), the mixturewas stirred at 30° C. for 16 h. Once the reaction was completed, thereaction mixture was then quenched by addition H₂O (10 mL) at 0° C., andthen diluted with H₂O (10 mL) and extracted with EtOAc (30 mL*2). Thecombined organic layers were washed with brine (30 mL), dried overNa₂SO₄, filtered and concentrated under reduced pressure to give aresidue. The liquid water was added with NaOH to adjust pH=9, quenchedwith aq NaCl, and then added with NaOH to adjust pH >14. The residue waspurified by HCl prep-HPLC to get the compoundN-[(1S)-1-[[(1S)-2-amino-2-cyano-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide(50 mg, 103.83 umol, 57.43% yield, 97.3% purity) as a solid. MS (ESI)m/z 469.2 [M+H]⁺

prep-HPLC condition:

column: Phenomenex luna C18 80*40 mm*3 um; mobile phase: [water (0.04%HCl)-ACN]; B %: 15%-40%, 7 min

¹H NMR (400 MHz, DMSO-d6) δ=11.59 (dd, J=1.9, 5.0 Hz, 1H), 9.16-8.58 (m,2H), 8.54-8.26 (m, 2H), 7.66 (d, J=9.0 Hz, 1H), 7.37 (dd, J=2.0, 4.2 Hz,1H), 7.14-7.06 (m, 1H), 7.04-6.97 (m, 1H), 6.51 (d, J=7.5 Hz, 1H),4.61-4.42 (m, 2H), 4.39-4.21 (m, 1H), 3.88 (s, 3H), 3.20-2.98 (m, 2H),2.48-2.34 (m, 1H), 2.14-1.88 (m, 2H), 1.82-1.47 (m, 5H), 0.92 (dd,J=6.0, 14.8 Hz, 6H)

Step for Compound 511:N-[(1S)-1-[[(1S)-2-cyano-2-(ethylamino)-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide

To a mixture ofN-[(1S)-1-[[(1S)-1-formyl-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide(80 mg, 108.47 umol, 60% purity, 1 eq) in DCM (5 mL) was added PdCl₂(3.85 mg, 21.69 umol, 0.2 eq), Na₂SO₄ (53.93 mg, 379.66 umol, 38.52 uL,3.5 eq), and ethanamine (9.78 mg, 216.95 umol, 14.19 uL, 2 eq). Theresulting mixture was stirred at 25° C. for 30 min, and then added withTMSCN (21.52 mg, 216.95 umol, 27.14 uL, 2 eq). The resulting mixture wasstirred at 25° C. for 1 h. Once the reaction was completed, the reactionmixture was filtered and concentrated under reduced pressure to give aresidue. The residue was purified by HCl prep-HPLC to yield 70 mg of themixture. The mixture was purified by SFC to get theN-[(1S)-1-[[(1S)-2-cyano-2-(ethylamino)-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide(16 mg, 28.20 umol, 26.00% yield, 87.525% purity) as an oil andN-[(1S)-1-[[(1S)-2-cyano-2-(ethylamino)-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide(16 mg, 31.44 umol, 28.98% yield, 97.569% purity) as a solid. MS (ESI)m/z 497.3 [M+H]⁺

Prep-HPLC condition:

column: Phenomenex luna C18 80*40 mm*3 um; mobile phase: [water (0.04%HCl)-ACN]; B %: 25%-40%, 7 min

SFC condition:

column: DAICEL CHIRALCEL OX (250 mm*30 mm, 10 um); mobile phase:[Neu-ETOH]; B %: 38%-38%, 9 min

Compound 511 Isomer 1: ¹H NMR (400 MHz, DMSO-d6) δ=11.56 (br s, 1H),8.37 (br d, J=7.7 Hz, 1H), 8.29-8.20 (m, 1H), 7.80-7.48 (m, 3H), 7.35(br d, J=2.0 Hz, 1H), 7.17-6.96 (m, 2H), 6.50 (d, J=7.7 Hz, 1H),4.53-4.40 (m, 1H), 4.05 (td, J=3.9, 7.7 Hz, 1H), 3.88 (s, 3H), 3.77 (brdd, J=4.9, 10.1 Hz, 1H), 3.18-2.97 (m, 2H), 2.88-2.63 (m, 2H), 2.40-2.24(m, 1H), 2.14-2.06 (m, 2H), 1.82-1.31 (m, 5H), 1.09-0.98 (m, 3H), 0.91(br dd, J=6.2, 16.1 Hz, 6H)

Compound 511 Isomer 2: ¹H NMR (400 MHz, DMSO-d6) δ=11.58 (d, J=1.5 Hz,1H), 8.41 (br d, J=7.9 Hz, 1H), 8.17 (br s, 1H), 7.63-7.50 (m, 1H), 7.37(d, J=1.8 Hz, 1H), 7.14-7.05 (m, 1H), 7.00 (d, J=8.2 Hz, 1H), 6.50 (d,J=7.5 Hz, 1H), 4.58-4.37 (m, 1H), 4.25-3.99 (m, 1H), 3.88 (s, 3H),3.81-3.51 (m, 1H), 3.16-2.96 (m, 2H), 2.89-2.54 (m, 2H), 2.43-2.23 (m,1H), 2.20-1.99 (m, 1H), 1.95-1.43 (m, 6H), 1.10-0.98 (m, 3H), 0.91 (dd,J=6.4, 15.2 Hz, 6H)

Step for Compound 507.N-[(1S)-1-[[(1S)-2-(benzylamino)-2-cyano-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide

To a mixture ofN-[(1S)-1-[[(1S)-1-formyl-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide(150 mg, 271.18 umol, 80% purity, 1 eq) in DCM (15 mL) was added PdCl₂(9.62 mg, 54.24 umol, 0.2 eq), Na₂SO₄ (134.82 mg, 949.14 umol, 96.30 uL,3.5 eq) and BnNH₂ (58.11 mg, 542.36 umol, 59.12 uL, 2 eq). The mixturewas stirred at 25° C. for 30 min, then added with TMSCN (53.81 mg,542.36 umol, 67.85 uL, 2 eq). The mixture was stirred at 25° C. for 2hours. Once the reaction was completed, the reaction mixture wasfiltered and concentrated under reduced pressure to give a residue. Theresidue was purified by HCl prep-HPLC to get the compoundN-[(1S)-1-[[(1S)-2-(benzylamino)-2-cyano-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide(30 mg, 51.71 umol, 19.07% yield, 96.291% purity) andN-[(1S)-1-[[(1S)-2-(benzylamino)-2-cyano-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]carbamoyl]-3-methyl-butyl]-4-methoxy-1H-indole-2-carboxamide (18 mg,31.04 umol, 11.44% yield, 96.329% purity) as a solid. MS (ESI) m/z 559.3[M+H]⁺

Prep-HPLC condition:

column: Phenomenex luna C18 80*40 mm*3 um; mobile phase: [water (0.04%HCl)-ACN]; B %: 38%-62%, 7 min

Compound 507 Isomer 1: ¹H NMR: (400 MHz, DMSO-d6) δ=11.58 (d, J=1.8 Hz,1H), 8.48-8.34 (m, 1H), 8.23 (br d, J=9.5 Hz, 1H), 7.69-7.53 (m, 1H),7.51-7.23 (m, 5H), 7.14-7.05 (m, 1H), 7.02-6.97 (m, 1H), 6.50 (d, J=7.7Hz, 1H), 4.56-4.37 (m, 1H), 4.23 (br d, J=9.3 Hz, 1H), 4.13-3.91 (m,2H), 3.88 (s, 3H), 3.84 (br d, J=13.2 Hz, 1H), 3.17-2.95 (m, 2H),2.42-2.24 (m, 1H), 2.16-1.98 (m, 1H), 1.93-1.44 (m, 6H), 0.90 (dd,J=6.3, 16.2 Hz, 6H)

Compound 507 Isomer 2: ¹H NMR (400 MHz, DMSO-d6) δ=11.56 (br d, J=1.5Hz, 1H), 8.52-8.14 (m, 2H), 7.69-7.55 (m, 1H), 7.49-7.22 (m, 6H),7.13-7.05 (m, 1H), 7.00 (d, J=8.4 Hz, 1H), 6.50 (d, J=7.5 Hz, 1H),4.56-4.41 (m, 1H), 4.21 (br s, 1H), 4.06-3.94 (m, 2H), 3.88 (s, 3H),3.83 (br d, J=12.8 Hz, 1H), 3.17-2.97 (m, 2H), 2.42-2.29 (m, 1H),2.17-2.00 (m, 2H), 1.83-1.44 (m, 5H), 0.90 (dd, J=6.3, 17.8 Hz, 6H)

Example 31. Synthesis of Viral Protease Inhibitor Compound 129

Step 1. 2-(trichloromethyl)-3H-imidazo[4,5-c]pyridine

To a solution of pyridine-3,4-diamine (2 g, 18.33 mmol, 1 eq) in AcOH(25 mL) was added methyl 2,2,2-trichloroethanimidate (3.88 g, 21.99mmol, 2.71 mL, 1.2 eq). The solution was stirred for 5 h at 100° C. Thereaction was added with H₂O (90 mL) and extracted with ethyl acetate (70mL*3) and washed with NaHCO₃ (90 mL*2). The organic layer was cautiouslyconcentrated to give crude 2-(trichloromethyl)-3H-imidazo[4,5-c]pyridine(800 mg, crude) was obtained as a yellow solid. The crude was useddirectly for the next step. MS (ESI) m/z 235.9 [M+H]⁺

Step 2: N-[(1S)-2-[[(1S)-1-cyano-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]amino]-1-(cyclopropylmethyl)-2-oxo-ethyl]-3H-imidazo[4,5-c]pyridine-2-carboxamide

To a solution of 2-(trichloromethyl)-3H-imidazo[4,5-c]pyridine (150 mg,634.29 umol, 1 eq) and(2S)-2-amino-N-[(1S)-1-cyano-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]-3-cyclopropyl-propanamide(167.66 mg, 634.29 umol, 1 eq) in THF (5 mL) and H₂O (2.5 mL) was addedNa₂CO₃ (201.68 mg, 1.90 mmol, 3 eq). The solution was stirred for 1 h at20° C. The solution was added with H₂O (20 mL), extracted with ethylacetate (40 mL*3) and concentrated to give crude. The crude was purifiedby pre-HPLC(Column: Waters Xbridge BEH C18 100*30 mm*10 um; mobilephase: [water (10 mM NH₄HCO₃)-ACN]; B %: 1%-23%, 8 min) to give 70%purity product and then continue purified by pre-HPLC(Column: PhenomenexLuna C18 75*30 mm*3 um; mobile phase: [water (0.2% FA)-ACN]; B %:1%-30%, 8 min) to give productN-[(1S)-2-[[(1S)-1-cyano-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]amino]-1-(cyclopropylmethyl)-2-oxo-ethyl]-3H-imidazo[4,5-c]pyridine-2-carboxamide(3 mg, 6.96 umol, 1.10% yield, 95% purity) was obtained as a solid. MS(ESI) m/z 410.1 [M+H]⁺. ¹H NMR (400 MHz, DMSO-d₆) δ=8.89-8.81 (m, 2H),8.77 (d, J=7.9 Hz, 1H), 8.21 (d, J=5.4 Hz, 2H), 7.54 (s, 1H), 7.43 (brd, J=5.4 Hz, 1H), 4.91-4.76 (m, 1H), 4.44-4.32 (m, 1H), 3.02-2.92 (m,2H), 2.25-2.16 (m, 1H), 2.03-1.91 (m, 2H), 1.78-1.38 (m, 4H), 0.59 (brs, 1H), 0.25 (br d, J=7.9 Hz, 2H), 0.05-0.11 (m, 2H).

Example 32. Synthesis of Viral Protease Inhibitor Compound 389A and 389B

Step 1: (S)-2-amino-3-((S)-2-oxopyrrolidin-3-yl)propanamide

tert-ButylN-[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]carbamate(2 g, 7.37 mmol, 1 eq) in HCl/EtOAc (4 M, 50 mL, 27.13 eq) was stirredat 25° C. for 1 h. Upon completion, the mixture was concentrated underthe reduced pressure affording the product(2S)-2-amino-3-[(3S)-2-oxopyrrolidin-3-yl]propanamide (1.2 g, crude) asa solid.

Step 2: Methyl 2-azaspiro[4.5]decane-3-carboxylate

A solution of 2-tert-butoxycarbonyl-2-azaspiro[4.5]decane-3-carboxylicacid (3 g, 10.59 mmol, 1 eq) in HCl/MeOH (4 M, 50 mL, 18.89 eq) wasstirred at 80° C. for 2 h. The mixture was concentrated under thereduced pressure to afford the product methyl2-azaspiro[4.5]decane-3-carboxylate (2 g, crude) as a yellow oil.

Step 3: Methyl2-(4-methoxy-1H-indole-2-carbonyl)-2-azaspiro[4.5]decane-3-carboxylate

To a solution of methyl 2-azaspiro[4.5]decane-3-carboxylate (2 g, 10.14mmol, 1 eq) and 4-methoxy-1H-indole-2-carboxylic acid (2.33 g, 12.17mmol, 1.2 eq) in DCM (30 mL) and DMF (5 mL) was added T3P (12.90 g,20.28 mmol, 12.06 mL, 50% purity, 2 eq) and DIEA (3.93 g, 30.41 mmol,5.30 mL, 3 eq). The mixture was stirred at 25° C. for 2 h. Uponcompletion, the reaction mixture was quenched by addition H₂O (100 mL),and extracted with DCM (50 mL*3). The combined organic layers werewashed with brine (50 mL), dried over Na₂SO₄, filtered and concentratedunder reduced pressure to give a residue. The residue was purified bycolumn chromatography (SiO₂, Petroleum ether:Ethyl acetate=10:1 to 0:1)to afford the product methyl2-(4-methoxy-1H-indole-2-carbonyl)-2-azaspiro[4.5]decane-3-carboxylate(3 g, 8.10 mmol, 79.88% yield) as a solid. MS (ESI) m/z 371.1 [M+H]⁺

Step 4:2-(4-methoxy-1H-indole-2-carbonyl)-2-azaspiro[4.5]decane-3-carboxylicacid

To a solution of methyl2-(4-methoxy-1H-indole-2-carbonyl)-2-azaspiro[4.5]decane-3-carboxylate(3 g, 8.10 mmol, 1 eq) in THF (45 mL) and H₂O (15 mL) was added LiOH.H₂O(1.70 g, 40.49 mmol, 5 eq). The mixture was stirred at 25° C. for 12 h.Upon completion, the mixture was quenched by addition H₂O (50 mL), andthen added aq. HCl (1 M) to adjust the pH=3-4, and then extracted withethyl acetate (50 mL*3). The combined organic layers were washed withbrine (30 mL), dried over Na₂SO₄, filtered and concentrated underreduced pressure affording the product2-(4-methoxy-1H-indole-2-carbonyl)-2-azaspiro[4.5]decane-3-carboxylicacid (2.6 g, crude) as a white solid. MS (ESI) m/z 357.1 [M+H]⁺

Step 5:N—((S)-1-amino-1-oxo-3-((S)-2-oxopyrrolidin-3-yl)propan-2-yl)-2-(4-methoxy-1H-indole-2-carbonyl)-2-azaspiro[4.5]decane-3-carboxamide

To a solution of2-(4-methoxy-1H-indole-2-carbonyl)-2-azaspiro[4.5]decane-3-carboxylicacid (1 g, 2.81 mmol, 1 eq) and(2S)-2-amino-3-[(3S)-2-oxopyrrolidin-3-yl]propanamide (720.49 mg, 4.21mmol, 1.5 eq) in DCM (30 mL) was added T3P (3.57 g, 5.61 mmol, 3.34 mL,50% purity, 2 eq) and DIEA (1.09 g, 8.42 mmol, 1.47 mL, 3 eq) at 0° C.The mixture was stirred at 30° C. for 1 h. Upon completion, the mixturewas quenched by addition H₂O (100 mL), and then extracted with DCM (50mL*3). The combined organic layers were washed with brine (50 mL), driedover Na₂SO₄, filtered and concentrated under reduced pressure to give aresidue. The residue was purified by column chromatography (SiO₂,DCM:MeOH=1:0 to 10:1) affording the productN-[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]-2-(4-methoxy-1H-indole-2-carbonyl)-2-azaspiro[4.5]decane-3-carboxamide(700 mg, 1.37 mmol, 48.96% yield) as a white solid. MS (ESI) m/z 510.3[M+H]⁺

Step 6:N—((S)-1-cyano-2-((S)-2-oxopyrrolidin-3-yl)ethyl)-2-(4-methoxy-1H-indole-2-carbonyl)-2-azaspiro[4.5]decane-3-carboxamide

To a solution ofN-[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]-2-(4-methoxy-1H-indole-2-carbonyl)-2-azaspiro[4.5]decane-3-carboxamide(700 mg, 1.37 mmol, 1 eq) in DCM (10 mL) was added Burgess reagent(982.03 mg, 4.12 mmol, 3 eq). The mixture was stirred at 25° C. for 2 h.Upon completion, the mixture was concentrated under the reduced pressureto give a residue. The residue was purified by prep-HPLC (column:Kromasil C18 (250*50 mm*10 um); mobile phase: [water (10 mMNH₄HCO₃)-ACN]; B %: 30%-60%, 10 min) affording the productN-[(1S)-1-cyano-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]-2-(4-methoxy-1H-indole-2-carbonyl)-2-azaspiro[4.5]decane-3-carboxamide(500 mg, 1.02 mmol, 74.05% yield) as a white solid. MS (ESI) m/z 492.3[M+H]⁺

Step 7:N—((S)-1-cyano-2-((S)-2-oxopyrrolidin-3-yl)ethyl)-2-(4-methoxy-1H-indole-2-carbonyl)-2-azaspiro[4.5]decane-3-carboxamide

N-[(1S)-1-cyano-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]-2-(4-methoxy-1H-indole-2-carbonyl)-2-azaspiro[4.5]decane-3-carboxamide(500 mg, 1.02 mmol) was separated by SFC (column: DAICEL CHIRALPAK AD(250 mm*30 mm, 10 um); mobile phase: [0.1% NH₃H₂O IPA]; B %: 55%-55%, 9min) to afford the productN-[(1S)-1-cyano-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]-2-(4-methoxy-1H-indole-2-carbonyl)-2-azaspiro[4.5]decane-3-carboxamide,Isomer 1 (264 mg, 537.04 umol, 52.80% yield) as a solid. MS (ESI) m/z492.3 [M+H]⁺; ¹H NMR (400 MHz, METHANOL-d₄) δ=7.28-6.76 (m, 3H),6.60-6.38 (m, 1H), 5.05 (br dd, J=5.2, 10.2 Hz, 1H), 4.63-4.60 (m, 1H),4.03-3.85 (m, 5H), 3.74-3.28 (m, 1H), 2.73 (br dd, J=5.0, 8.6 Hz, 1H),2.51-2.28 (m, 2H), 2.27-2.08 (m, 1H), 1.96-1.72 (m, 2H), 1.69-1.38 (m,11H), 1.37-1.09 (m, 1H); and

N-[(1S)-1-cyano-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]-2-(4-methoxy-1H-indole-2-carbonyl)-2-azaspiro[4.5]decane-3-carboxamide,Isomer 2 (140 mg, 284.51 umol, 27.97% yield) as a solid. MS (ESI) m/z492.3 [M+H]⁺; ¹H NMR (400 MHz, METHANOL-d₄) δ=7.30-6.81 (m, 3H), 6.53(br d, J=2.0 Hz, 1H), 5.12-4.95 (m, 2H), 4.70-4.55 (m, 2H), 4.08-3.86(m, 4H), 3.84-3.72 (m, 1H), 2.62-2.40 (m, 1H), 2.36-2.18 (m, 2H),1.94-1.69 (m, 3H), 1.68-1.34 (m, 11H).

Example 33. Synthesis of Viral Protease Inhibitor Compound 399

Step 1: (S)-methyl 2-amino-3-((S)-2-oxopyrrolidin-3-yl)propanoatehydrochloride

To a solution of methyl(2S)-2-(tert-butoxycarbonylamino)-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(130 mg, 454.03 umol, 1 eq) in HCl/dioxane (4 M, 2.27 mL, 20 eq) wasstirred at 25° C. for 0.5 h. The reaction mixture was concentrated underreduced pressure to get the product methyl(2S)-2-amino-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate (173.4 mg, 451.67umol, 99.48% yield, HCl) was obtained as yellow liquid.

Step 2: (S)-tert-butyl7-(((S)-1-methoxy-1-oxo-3-((S)-2-oxopyrrolidin-3-yl)propan-2-yl)carbamoyl)-6-azaspiro[3.4]octane-6-carboxylate

To a solution of(7S)-6-tert-butoxycarbonyl-6-azaspiro[3.4]octane-7-carboxylic acid(105.34 mg, 412.59 umol, 1 eq) and methyl(2S)-2-amino-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate (158.4 mg, 412.59umol, 1 eq, HCl) in DCM (1.2 mL) and DMF (0.4 mL) was added DMAP (100.81mg, 825.19 umol, 2 eq) and EDCI (158.19 mg, 825.19 umol, 2 eq). Thereaction mixture was stirred at 25° C. for 1 h. The residue was dilutedwith H₂O (6 mL) and extracted with ethyl acetate (3 mL). The combinedorganic layers were washed with ethyl acetate (3 mL*3), dried overNa₂SO₄, filtered and concentrated under reduced pressure to give aresidue. The residue was purified by prep-TLC (SiO₂, petroleumether/ethyl acetate=0/1) to get the product tert-butyl(7S)-7-[[(1S)-2-methoxy-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]carbamoyl]-6-azaspiro[3.4]octane-6-carboxylate(66.3 mg, 156.55 umol, 37.94% yield) was obtained as a liquid. MS (ESI)m/z 424.0 [M+H]⁺

Step 3: (S)-methyl3-((S)-2-oxopyrrolidin-3-yl)-2-((S)-6-azaspiro[3.4]octane-7-carboxamido)propanoate

A solution of tert-butyl(7S)-7-[[(1S)-2-methoxy-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]carbamoyl]-6-azaspiro[3.4]octane-6-carboxylate(66.3 mg, 156.55 umol, 1 eq) in HCl/MeOH (4 M, 782.76 uL, 20 eq) wasstirred at 25° C. for 0.5 h. The reaction mixture was concentrated underreduced pressure to get the product methyl(2S)-2-[[(7S)-6-azaspiro[3.4]octane-7-carbonyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(71.1 mg, 156.09 umol, 99.71% yield, 79% purity, HCl) was obtained as ayellow liquid.

Step 4: (S)-methyl2-((S)-6-(4-methoxy-1H-indole-2-carbonyl)-6-azaspiro[3.4]octane-7-carboxamido)-3-((S)-2-oxopyrrolidin-3-yl)propanoate

To a solution of methyl(2S)-2-[[(7S)-6-azaspiro[3.4]octane-7-carbonyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(62.8 mg, 137.87 umol, 1 eq, HCl) and 4-methoxy-1H-indole-2-carboxylicacid (26.36 mg, 137.87 umol, 1 eq) in DCM (1.2 mL) and DMF (0.4 mL) wasadded DMAP (33.69 mg, 275.74 umol, 2 eq) and EDCI (52.86 mg, 275.74umol, 2 eq) at 25° C. for 1 h. The residue was diluted with brine (6 mL)and extracted with ethyl acetate (3 mL*3). The combined organic layerswere dried over Na₂SO₄, filtered and concentrated under reduced pressureto give a residue. The residue was purified by prep-TLC (SiO₂, petroleumether/ethyl acetate=0/1) to get the product methyl(2S)-2-[[(7S)-6-(4-methoxy-1H-indole-2-carbonyl)-6-azaspiro[3.4]octane-7-carbonyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(33.2 mg, 66.86 umol, 48.50% yield) was obtained as a white solid. MS(ESI) m/z 497.1 [M+H]⁺

Step 5:(S)—N—((S)-1-amino-1-oxo-3-((S)-2-oxopyrrolidin-3-yl)propan-2-yl)-6-(4-methoxy-1H-indole-2-carbonyl)-6-azaspiro[3.4]octane-7-carboxamide

A mixture of methyl(2S)-2-[[(7S)-6-(4-methoxy-1H-indole-2-carbonyl)-6-azaspiro[3.4]octane-7-carbonyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(23.0 mg, 46.32 umol, 1 eq) and ammonia (7 M, 4 mL, 604.50 eq) wasstirred at 25° C. for 16 h. The reaction mixture was concentrated underreduced pressure to get the product(7S)—N-[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]-6-(4-methoxy-1H-indole-2-carbonyl)-6-azaspiro[3.4]octane-7-carboxamide(15 mg, crude) was obtained as a yellow solid. MS (ESI) m/z 482.2 [M+H]⁺

Step 6:(S)—N—((S)-1-cyano-2-((S)-2-oxopyrrolidin-3-yl)ethyl)-6-(4-methoxy-1H-indole-2-carbonyl)-6-azaspiro[3.4]octane-7-carboxamide

A solution of(7S)—N-[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]-6-(4-methoxy-1H-indole-2-carbonyl)-6-azaspiro[3.4]octane-7-carboxamide(15 mg, 28.66 umol, 1 eq) and Burgess reagent (13.66 mg, 57.32 umol, 2eq) was stirred at 25° C. for 24 h. The reaction mixture wasconcentrated under reduced pressure to give a residue. The residue waspurified by prep-HPLC (column: Waters Xbridge BEH C18 100*30 mm*10 um;mobile phase: [water (10 mM NH₄HCO₃)-ACN]; B %: 20%-45%, 8 min) to getthe product(7S)—N-[(1S)-1-cyano-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]-6-(4-methoxy-1H-indole-2-carbonyl)-6-azaspiro[3.4]octane-7-carboxamide(3.01 mg, 6.49 umol, 22.66% yield) was obtained as a solid. MS (ESI) m/z464.3 [M+H]⁺ ¹H NMR (400 MHz, METHANOL-d₄) δ ppm 6.95-7.24 (m, 3H)6.47-6.58 (m, 1H) 5.01 (br dd, J=10.67, 5.19 Hz, 1H) 4.58 (t, J=7.09 Hz,1H) 3.82-4.19 (m, 5H) 3.19 (br t, J=8.52 Hz, 1H) 2.93-3.07 (m, 1H)2.28-2.56 (m, 3H) 2.16-2.27 (m, 2H) 1.94-2.14 (m, 6H) 1.47-1.86 (m, 2H).

Example 34. Synthesis of Viral Protease Inhibitor Compound 405

Step 1: methyl(2S)-2-[[(2S)-2-(tert-butoxycarbonylamino)-4,4-dimethyl-pentanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate

To a solution of methyl(2S)-2-amino-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate (225 mg, 1.21 mmol,1 eq) in DMF (2 mL) and DCM (4 mL) was added TEA (733.62 mg, 7.25 mmol,1.01 mL, 6 eq) and T3P (1.15 g, 3.62 mmol, 1.08 mL, 3 eq) and(2S)-2-(tert-butoxycarbonylamino)-4,4-dimethyl-pentanoic acid (296.42mg, 1.21 mmol, 1 eq). The solution was stirred for 1 h at 25° C. Thereaction was added with H₂O (40 mL) and extracted with ethyl acetate (50mL*3) and the organic layer was cautiously concentrated to give crudecompound methyl(2S)-2-[[(2S)-2-(tert-butoxycarbonylamino)-4,4-dimethyl-pentanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(440 mg, crude) as a solid used directly for the next step. MS (ESI) m/z414.1 [M+H]⁺

Step 2: methyl(2S)-2-[[(2S)-2-amino-4,4-dimethyl-pentanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate

A solution of methyl(2S)-2-[[(2S)-2-(tert-butoxycarbonylamino)-4,4-dimethyl-pentanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(440 mg, 1.06 mmol, 1 eq) in HCl/MeOH (10 mL) was stirred for 1 h at 25°C. TLC(DCM:MeOH=10:1). The reaction was cautiously concentrated to givecrude. Compound methyl(2S)-2-[[(2S)-2-amino-4,4-dimethyl-pentanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(310 mg, crude) as a solid used directly for the next step. MS (ESI) m/z314.3 [M+H]⁺

Step 3: methyl(2S)-2-[[(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4,4-dimethyl-pentanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate

To a solution of methyl(2S)-2-[[(2S)-2-amino-4,4-dimethyl-pentanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(310 mg, 989.18 umol, 1 eq) in DMF (4 mL) and DCM (4 mL) was added EDCI(379.25 mg, 1.98 mmol, 2 eq) and DMAP (241.70 mg, 1.98 mmol, 2 eq) and4-methoxy-1H-indole-2-carboxylic acid (189.11 mg, 989.18 umol, 1 eq) wasadded. The solution was stirred for 3 h at 25° C. The reaction was addedwith H₂O (40 mL) and extracted with ethyl acetate (80 mL*3) and theorganic layer was cautiously concentrated to give crude. The crude waspurified by pre-TLC(SiO₂, ethyl acetate:MeOH=10:1) to afford methyl(2S)-2-[[(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4,4-dimethyl-pentanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(200 mg, 411.05 umol, 41.55% yield). MS (ESI) m/z 487.2 [M−H]⁺

Step 4:N-[(1S)-1-[[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]carbamoyl]-3,3-dimethyl-butyl]-4-methoxy-1H-indole-2-carboxamide

A solution of methyl(2S)-2-[[(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4,4-dimethyl-pentanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(135 mg, 277.46 umol, 1 eq) in NH₃/MeOH (7 M, 8 mL, 201.83 eq) wasstirred for 16 h at 65° C. The reaction was cautiously concentrated togive crude. CompoundN-[(1S)-1-[[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]carbamoyl]-3,3-dimethyl-butyl]-4-methoxy-1H-indole-2-carboxamide(130 mg, crude) as a solid used directly for the next step. MS (ESI) m/z472.3 [M+H]⁺; Prep-HPLC condition: column: Phenomenex Gemini-NX C1875*30 mm*3 um; mobile phase: [water (0.05% NH₃H₂O+10 mM NH₄HCO₃)-ACN]; B%: 35%-55%, 8 min

Step 5:N-[(1S)-1-[[(1S)-1-cyano-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]carbamoyl]-3,3-dimethyl-butyl]-4-methoxy-1H-indole-2-carboxamide

To a solution ofN-[(1S)-1-[[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]carbamoyl]-3,3-dimethyl-butyl]-4-methoxy-1H-indole-2-carboxamide(130 mg, 275.69 umol, 1 eq) in DCM (7 mL) was added Burgess reagent(197.09 mg, 827.06 umol, 3 eq). The solution was stirred for 1 h at 25°C. The reaction was cautiously concentrated to give crude. The crude waspurified by pre-HPLC(TFA) to affordN-[(1S)-1-[[(1S)-1-cyano-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]carbamoyl]-3,3-dimethyl-butyl]-4-methoxy-1H-indole-2-carboxamide(36 mg, 75.41 umol, 27.35% yield, 95% purity) as a solid. MS (ESI) m/z454.1 [M+H]⁺. Prep-HPLC condition: column: Phenomenex luna C18 80*40mm*3 um; mobile phase: [water (0.04% HCl)-ACN]; B %: 30%-55%, 7 min; ¹HNMR (400 MHz, METHANOL-d₄) δ ppm 1.02 (s, 9H) 1.74-1.94 (m, 4H)2.21-2.37 (m, 2H) 2.52-2.63 (m, 1H) 3.16-3.26 (m, 2H) 3.92 (s, 3H) 4.63(dd, J=8.49, 4.30 Hz, 1H) 4.98-5.06 (m, 1H) 6.50 (d, J=7.72 Hz, 1H) 7.02(d, J=8.38 Hz, 1H) 7.10-7.16 (m, 1H) 7.23 (d, J=0.88 Hz, 1H).

Example 35. Synthesis of Viral Protease Inhibitor Compound 491 and 491A

Step 1: Methyl(2S)-2-[[3-cyclopropyl-2-[(4-methoxy-1H-indole-2-carbonyl)amino]propanoyl]amino]-3-[(3S)-2-oxo-3-piperidyl]propanoate

To the mixture of methyl(2S)-2-amino-3-[(3S)-2-oxo-3-piperidyl]propanoate (1 g, 4.22 mmol, 1 eq,HCl), 3-cyclopropyl-2-[(4-methoxy-1H-indole-2-carbonyl)amino]propanoicacid (1.5 g, 5.06 mmol, 1.2 eq, HCl) and TEA (1.7 g, 16.88 mmol, 2.35mL, 4 eq) in DMF (5 mL) was added T3P (5.3 g, 8.44 mmol, 5.02 mL, 50%purity, 2 eq) at 25° C. The mixture was stirred at 25° C. for 16 h. TLC(DCM:MeOH=10:1/UV254 nm) showed new spot was detected. The reactionmixture was diluted with H₂O (10 mL) and the mixture was extracted withethyl acetate (10 mL*3). The combined organic phase was washed withbrine (10 mL*2), dried with anhydrous Na₂SO₄, filtered and concentratedin vacuum. The residue was purified by flash silica gel chromatography(ISCO®; 12 g SepaFlash® Silica Flash Column, Eluent of 100-25% Ethylacetate/MeOH@ 30 mL/min). Compound methyl(2S)-2-[[3-cyclopropyl-2-[(4-methoxy-1H-indole-2-carbonyl)amino]propanoyl]amino]-3-[(3S)-2-oxo-3-piperidyl]propanoate(1.9 g, 3.84 mmol, 91.0% yield) was obtained as a solid. Methyl(2S)-2-[[(2S)-3-cyclopropyl-2-[(4-methoxy-1H-indole-2-carbonyl)amino]propanoyl]amino]-3-[(3S)-2-oxo-3-piperidyl]propanoate(50 mg, 0.10 mmol, 1 eq) was purified by prep-HPLC (column: PhenomenexGemini-NX 80*30 mm*3 um; mobile phase: [water (0.05% NH₃H₂O+10 mMNH₄HCO₃)-ACN]; B %: 20%-50%, 9.5 min). Compound methyl(2S)-2-[[(2S)-3-cyclopropyl-2-[(4-methoxy-1H-indole-2-carbonyl)amino]propanoyl]amino]-3-[(3S)-2-oxo-3-piperidyl]propanoate(50 mg, 0.10 mmol, 1 eq) was obtained as a solid.

Step 2:N-[2-[[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxo-3-piperidyl]methyl]ethyl]amino]-1-(cyclopropylmethyl)-2-oxo-ethyl]-4-methoxy-1H-indole-2-carboxamide

The mixture of methyl(2S)-2-[[3-cyclopropyl-2-[(4-methoxy-1H-indole-2-carbonyl)amino]propanoyl]amino]-3-[(3S)-2-oxo-3-piperidyl]propanoate(1.00 g, 1.73 mmol, 84% purity, 1 eq) in NH₃ (7 M, 24.77 mL, 100 eq) (7Min MeOH) was stirred at 80° C. for 36 h. Then, the reaction mixture wasconcentrated in vacuum. CompoundN-[2-[[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxo-3-piperidyl]methyl]ethyl]amino]-1-(cyclopropylmethyl)-2-oxo-ethyl]-4-methoxy-1H-indole-2-carboxamide(813 mg, crude) was obtained as yellow solid.

N-[(1S)-2-[[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxo-3-piperidyl]methyl]ethyl]amino]-1-(cyclopropylmethyl)-2-oxo-ethyl]-4-methoxy-1H-indole-2-carboxamide(50 mg, 0.10 mmol, 1 eq) was purified by prep-HPLC (column: PhenomenexGemini-NX 80*40 mm*3 um; mobile phase: [water (0.05% NH₃H₂O+10 mMNH₄HCO₃)-ACN]; B %: 23%-53%, 7.8 min). CompoundN-[(1S)-2-[[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxo-3-piperidyl]methyl]ethyl]amino]-1-(cyclopropylmethyl)-2-oxo-ethyl]-4-methoxy-1H-indole-2-carboxamide(20.3 mg, 42.5 umol, 39.9% yield, 98.4% purity) was obtained as whitesolid.

Step 3:N-[2-[[(1S)-1-cyano-2-[(3S)-2-oxo-3-piperidyl]ethyl]amino]-1-(cyclopropylmethyl)-2-oxo-ethyl]-4-methoxy-1H-indole-2-carboxamide

A mixture ofN-[2-[[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxo-3-piperidyl]methyl]ethyl]amino]-1-(cyclopropylmethyl)-2-oxo-ethyl]-4-methoxy-1H-indole-2-carboxamide(663.0 mg, 1.41 mmol, 1 eq) andmethoxycarbonyl-(triethylammonio)sulfonyl-azanide (673.0 mg, 2.82 mmol,2 eq) in DCM (8 mL) was stirred at 25° C. for 16 h. Then,methoxycarbonyl-(triethylammonio)sulfonyl-azanide (336.5 mg, 1.41 mmol,1 eq) was added at the mixture and the mixture was stirred at 25° C. for16 hr. LC-MS showed that the desired compound was detected. TLC(petroleum ether: ethyl acetate=0:1/I2) showed new spots were detected.The reaction mixture was diluted with H₂O (10 mL) and the mixture wasextracted with ethyl acetate (10 mL*3). The combined organic phase waswashed with brine (10 mL*2), dried with anhydrous Na₂SO₄, filtered andconcentrated in vacuum. The residue was purified by prep-HPLC (column:Phenomenex Gemini-NX 80*30 mm*3 um; mobile phase: [water (0.05%NH₃H₂O+10 mM NH₄HCO₃)-ACN]; B %: 23%-53%, 9.5 min). CompoundN-[2-[[(1S)-1-cyano-2-[(3S)-2-oxo-3-piperidyl]ethyl]amino]-1-(cyclopropylmethyl)-2-oxo-ethyl]-4-methoxy-1H-indole-2-carboxamide(450 mg, 0.98 mmol, 69.9% yield) was obtained as yellow solid.

Step 4:N-[(1S)-2-[[(1S)-1-cyano-2-[(3S)-2-oxo-3-piperidyl]ethyl]amino]-1-(cyclopropylmethyl)-2-oxo-ethyl]-4-methoxy-1H-indole-2-carboxamide

N-[2-[[1-cyano-2-[(3S)-2-oxo-3-piperidyl]ethyl]amino]-1-(cyclopropylmethyl)-2-oxo-ethyl]-4-methoxy-1H-indole-2-carboxamide(550.0 mg, 1.22 mmol, 1 eq) was purified by SFC (column: DAICELCHIRALPAK AD (250 mm*30 mm, 10 um); mobile phase: [0.1% NH₃H₂O ETOH]; B%: 55%-55%, min). CompoundN-[(1S)-2-[[(1S)-1-cyano-2-[(3S)-2-oxo-3-piperidyl]ethyl]amino]-1-(cyclopropylmethyl)-2-oxo-ethyl]-4-methoxy-1H-indole-2-carboxamide,Isomer 1 (147.1 mg, 0.25 mmol, 22.1% yield) was obtained as a solid.LCMS: Rt=0.756 min; for C₂₄H₂₉N₅O₄ MS Calcd: 451.22, MS Found: 452.1[M+H⁺]. ¹H NMR (400 MHz, DMSO-d₆) δ 11.56 (br s, 1H), 8.90 (br d, J=8.0Hz, 1H), 8.49 (br d, J=7.4 Hz, 1H), 7.52 (br s, 1H), 7.36 (s, 1H),7.12-7.06 (m, 1H), 7.03-6.98 (m, 1H), 6.50 (d, J=7.6 Hz, 1H), 5.17-4.96(m, 1H), 4.56-4.33 (m, 1H), 3.88 (s, 3H), 3.09 (br s, 2H), 2.33-2.19 (m,2H), 1.88-1.76 (m, 3H), 1.70 (br dd, J=3.8, 8.3 Hz, 1H), 1.57 (br s,1H), 1.50-1.35 (m, 2H), 0.80 (br s, 1H), 0.41 (br d, J=6.6 Hz, 2H),0.25-0.03 (m, 2H); and

N-[(1R)-2-[[(1S)-1-cyano-2-[(3S)-2-oxo-3-piperidyl]ethyl]amino]-1-(cyclopropylmethyl)-2-oxo-ethyl]-4-methoxy-1H-indole-2-carboxamidem,Isomer 2 (113.1 mg, 0.32 mmol, 28.8% yield, 100% purity) was obtained asa solid. LCMS: Rt=0.761 min; for C₂₄H₂₉N₅O₄ MS Calcd: 451.22, MS Found:452.0 [M+H⁺]. ¹H NMR (400 MHz, DMSO-d₆) δ 11.57 (s, 1H), 8.89 (br d,J=8.0 Hz, 1H), 8.49 (br d, J=7.6 Hz, 1H), 7.51 (br s, 1H), 7.36 (d,J=1.6 Hz, 1H), 7.13-7.06 (m, 1H), 7.03-6.97 (m, 1H), 6.50 (d, J=7.5 Hz,1H), 5.08-4.99 (m, 1H), 4.52-4.42 (m, 1H), 3.88 (s, 3H), 3.08 (br s,2H), 2.23-2.13 (m, 2H), 1.90-1.68 (m, 4H), 1.64-1.36 (m, 3H), 0.85-0.70(m, 1H), 0.45-0.33 (m, 2H), 0.24-0.11 (m, 1H), 0.13-0.03 (m, 1H).

Example 36. Synthesis of Viral Protease Inhibitor Compound 531

Step 1: methyl(2S)-2-[[(2S)-2-[(7-chloro-1H-indole-2-carbonyl)amino]-3-cyclopropyl-propanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate

To a mixture of methyl(2S)-2-[[(2S)-2-amino-3-cyclopropyl-propanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(500 mg, 1.68 mmol, 1 eq) in DCM (10 mL) and DMF (2.5 mL), was addedDMAP (616.30 mg, 5.04 mmol, 3 eq) in one portion at 25° C. The mixturewas added 7-chloro-1H-indole-2-carboxylic acid (394.69 mg, 2.02 mmol,1.2 eq) and EDCI (967.04 mg, 5.04 mmol, 3 eq). The resulting mixture wasstirred at 25° C. for 2 h. Then, the mixture was concentrated underreduced pressure to give the crude product. The crude was purified bycolumn chromatography (SiO₂, Petroleum ether/Ethyl acetate=5/1 to 0/1)to give methyl(2S)-2-[[(2S)-2-[(7-chloro-1H-indole-2-carbonyl)amino]-3-cyclopropyl-propanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(550 mg, 1.16 mmol, 68.87% yield) as a white solid. MS (ESI) m/z 475.1[M+H]⁺

Step 2:N-[(1S)-2-[[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]amino]-1-(cyclopropylmethyl)-2-oxo-ethyl]-7-chloro-1H-indole-2-carboxamide

A mixture of methyl(2S)-2-[[(2S)-2-[(7-chloro-1H-indole-2-carbonyl)amino]-3-cyclopropyl-propanoyl]amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propanoate(500 mg, 1.05 mmol, 1 eq) in NH₃/MeOH (7 M, 10 mL, 66.49 eq) was stirredat 60° C. for 16 h. The reaction mixture was concentrated under reducedpressure to giveN-[(1S)-2-[[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]amino]-1-(cyclopropylmethyl)-2-oxo-ethyl]-7-chloro-1H-indole-2-carboxamide(440 mg, 956.68 umol, 90.87% yield) as a solid. MS (ESI) m/z 460.3[M+H]⁺

Step 3: 7-chloro-N-[(1S)-2-[[(1S)-1-cyano-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]amino]-1-(cyclopropylmethyl)-2-oxo-ethyl]-1H-indole-2-carboxamide

To a mixture ofN-[(1S)-2-[[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxopyrrolidin-3-yl]methyl]ethyl]amino]-1-(cyclopropylmethyl)-2-oxo-ethyl]-7-chloro-1H-indole-2-carboxamide(430 mg, 934.94 umol, 1 eq) in DCM (6 mL) was added Burgess reagent(445.61 mg, 1.87 mmol, 2 eq) in one portion at 25° C. The mixture wasstirred at 25° C. for 4 h. The reaction mixture was concentrated underreduced pressure to give the crude product. The crude was purified byprep-HPLC (column: Phenomenex Gemini-NX C18 75*30 mm*3 um; mobile phase:[water (0.05% NH₃H₂O+10 mM NH₄HCO₃)-ACN]; B %: 30%-60%, 8 min) to give7-chloro-N-[(1S)-2-[[(1S)-1-cyano-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]amino]-1-(cyclopropylmethyl)-2-oxo-ethyl]-1H-indole-2-carboxamide(180 mg, 407.32 umol, 43.57% yield) as a solid. MS (ESI) m/z 442.2[M+H]; ¹H NMR (400 MHz, DMSO-d₆) δ=11.71 (br s, 1H), 9.01 (d, J=7.9 Hz,1H), 8.72 (d, J=7.5 Hz, 1H), 7.71 (s, 1H), 7.63 (dd, J=0.7, 7.9 Hz, 1H),7.34-7.25 (m, 2H), 7.07 (t, J=7.8 Hz, 1H), 5.00 (q, J=7.9 Hz, 1H),4.58-4.49 (m, 1H), 3.13 (quin, J=9.2 Hz, 2H), 2.42-2.31 (m, 1H),2.22-2.05 (m, 2H), 1.89-1.64 (m, 3H), 1.57-1.46 (m, 1H), 0.89-0.75 (m,1H), 0.50-0.37 (m, 2H), 0.25-0.07 (m, 2H).

Example 37. Synthesis of Viral Protease Inhibitor Compound 635

Step 1:(2S)-2-amino-N-[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxo-3-piperidyl]methyl]ethyl]-3-cyclopropyl-propanamide

To a solution of benzylN-[(1S)-2-[[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxo-3-piperidyl]methyl]ethyl]amino]-1-(cyclopropylmethyl)-2-oxo-ethyl]carbamate(400 mg, 0.92 mmol, 1 eq) in MeOH (5 mL) was added Pd (200 mg, 10%purity) and H₂ (0.92 mmol). The mixture was stirred at 25° C. under 15psi for 1 hr. The mixture was filtered to give the filter liquor. Themixture was concentrated under reduce pressure to give compound(2S)-2-amino-N-[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxo-3-piperidyl]methyl]ethyl]-3-cyclopropyl-propanamide(274 mg, 0.92 mmol, 99.5% yield) as a solid.

Step 2:N-[(1S)-2-[[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxo-3-piperidyl]methyl]ethyl]amino]-1-(cyclopropylmethyl)-2-oxo-ethyl]-6-chloro-1H-indole-2-carboxamide

To a solution of(2S)-2-amino-N-[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxo-3-piperidyl]methyl]ethyl]-3-cyclopropyl-propanamide(137 mg, 0.46 mmol, 1 eq) and 6-chloro-1H-indole-2-carboxylic acid (90.4mg, 0.46 mmol, 1 eq) in DMF (2 mL) was added DIPEA (119.4 mg, 0.92 mmol,0.16 mL, 2 eq) and HATU (210.9 mg, 0.55 mmol, 1.2 eq). The mixture wasstirred at 25° C. for 1 hr. LCMS showed one peak with desired MS wasdetected. The mixture was concentrated under reduce pressure. Theresidue was purified by flash silica gel chromatography (ISCO®; 12 gSepaFlash® Silica Flash Column, Eluent of 0-10% DCM/MeOH @ 30 mL/min) togive CompoundN-[(1S)-2-[[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxo-3-piperidyl]methyl]ethyl]amino]-1-(cyclopropylmethyl)-2-oxo-ethyl]-6-chloro-1H-indole-2-carboxamide(200 mg, 89.0% yield) as a solid. LCMS: Rt=0.780 min; for C₂₃H₂₈ClN₅O₄MS Calcd.: 473.18; MS Found: 474.1 [M+H⁺].

Step 3:6-Chloro-N-[(1S)-2-[[(1S)-1-cyano-2-[(3S)-2-oxo-3-piperidyl]ethyl]amino]-1-(cyclopropylmethyl)-2-oxo-ethyl]-1H-indole-2-carboxamide

To a solution ofN-[(1S)-2-[[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxo-3-piperidyl]methyl]ethyl]amino]-1-(cyclopropylmethyl)-2-oxo-ethyl]-6-chloro-1H-indole-2-carboxamide(47.5 mg, 0.1 mmol, 1 eq) in DCM (1 mL) was added Burgess reagent (71.6mg, 0.3 mmol, 3 eq) at 0° C. The mixture was stirred at 25° C. for 12hr. The mixture was concentrated under reduce pressure. The residue waspurified by prep-HPLC (column: Phenomenex Gemini-NX 80*40 mm*3 um;mobile phase: [water (0.05% NH₃H₂O+10 mM NH₄HCO₃)-ACN]; B %: 31%-61%,7.8 min) to give compound6-chloro-N-[(1S)-2-[[(1S)-1-cyano-2-[(3S)-2-oxo-3-piperidyl]ethyl]amino]-1-(cyclopropylmethyl)-2-oxo-ethyl]-1H-indole-2-carboxamide(64.33 mg, 34.7% yield) as a solid. LCMS: Rt=0.832 min; forC₂₃H₂₆ClN₅O₃; MS Calcd.: 455.17; MS Found: 456.1 [M+H⁺]. ¹H NMR (400MHz, DMSO-d₆) δ 11.73 (br s, 1H), 8.95 (br d, J=8.0 Hz, 1H), 8.66 (br d,J=7.5 Hz, 1H), 7.66 (d, J=8.5 Hz, 1H), 7.53 (br s, 1H), 7.44 (s, 1H),7.31 (s, 1H), 7.05 (dd, J=1.8, 8.5 Hz, 1H), 5.11-4.96 (m, 1H), 4.52-4.42(m, 1H), 3.09 (br s, 2H), 2.34-2.21 (m, 2H), 1.89-1.75 (m, 3H),1.74-1.65 (m, 1H), 1.56 (br s, 1H), 1.51-1.29 (m, 2H), 0.79 (br s, 1H),0.42 (br d, J=7.0 Hz, 2H), 0.23-0.01 (m, 2H)

Example 38. Synthesis of Viral Protease Inhibitor Compound 637

Step 1: 4,7-Dichloro-2-(trichloromethyl)-1H-benzimidazole

To a solution of 3,6-dichlorobenzene-1,2-diamine (0.3 g, 1.69 mmol, 1eq) in AcOH (12.57 g, 209.2 mmol, 11.97 mL, 123.8 eq) was added methyl2,2,2-trichloroacetimidate (313.0 mg, 1.77 mmol, 0.21 mL, 1.05 eq) at 0°C. The mixture was stirred at 25° C. for 16 hr. The resulting mixturewas diluted with H₂O (40 mL) and filtered to give4,7-dichloro-2-(trichloromethyl)-1H-benzo[d]imidazole (300 mg, crude) asa solid.

Step 2: 4,7-Dichloro-1H-benzimidazole-2-carboxylic acid

To a solution of NaOH (0.8 g, 20.0 mmol, 20.2 eq) in H₂O (10 mL) wasadded 4,7-dichloro-2-(trichloromethyl)-1H-benzo[d]imidazole (0.3 g,985.58 umol, 1 eq) at 0° C. The mixture was stirred at 25° C. for 1 hr.The pH of the mixture was adjusted with HCl (2 M) to pH=2-3 and then themixture was filtered to give4,7-dichloro-1H-benzo[d]imidazole-2-carboxylic acid (0.2 g, crude) as asolid.

Step 3:N-[(1S)-2-[[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxo-3-piperidyl]methyl]ethyl]amino]-1-(cyclopropylmethyl)-2-oxo-ethyl]-4,6-dichloro-1H-benzimidazole-2-carboxamide

To a solution of(S)-2-amino-N—((S)-1-amino-1-oxo-3-((S)-2-oxopiperidin-3-yl)propan-2-yl)-3-cyclopropylpropanamide(130 mg, 0.43 mmol, 1 eq) and4,7-dichloro-1H-benzo[d]imidazole-2-carboxylic acid (101.3 mg, 0.43mmol, 1.0 eq) in DMF (3 mL) was added HATU (250.1 mg, 0.65 mmol, 1.5 eq)and DIPEA (113.3 mg, 0.87 mmol, 0.15 mL, 2.0 eq). The mixture wasstirred at 25° C. for 1 hr. TLC (Dichloromethane: Methanol=10/1)indicated 4,7-dichloro-1H-benzo[d]imidazole-2-carboxylic acid wasconsumed completely and one new spot formed. The reaction mixture wasconcentrated under reduced pressure to give a residue. The residue waspurified by column chromatography (SiO₂, Petroleum ether/Ethylacetate=100/1 to 10/1) to giveN—((S)-1-(((S)-1-amino-1-oxo-3-((S)-2-oxopiperidin-3-yl)propan-2-yl)amino)-3-cyclopropyl-1-oxopropan-2-yl)-4,7-dichloro-1H-benzo[d]imidazole-2-carboxamide(0.2 g, 0.39 mmol, 89% yield) as a solid.

Step 4:4,7-dichloro-N-[(1S)-2-[[(1S)-1-cyano-2-[(3S)-2-oxo-3-piperidyl]ethyl]amino]-1-(cyclopropylmethyl)-2-oxo-ethyl-1H-benzimidazole-2-carboxamide

To a solution ofN—((S)-1-(((S)-1-amino-1-oxo-3-((S)-2-oxopiperidin-3-yl)propan-2-yl)amino)-3-cyclopropyl-1-oxopropan-2-yl)-4,7-dichloro-1H-benzo[d]imidazole-2-carboxamide(100.00 mg, 0.19 mmol, 1 eq) in DCM (3.0 mL) was added Burgess Reagent(140.3 mg, 0.58 mmol, 3.0 eq). The mixture was stirred at 25° C. for 1hr. The reaction mixture was concentrated under reduced pressure to givea residue. The residue was purified by prep-HPLC (column: PhenomenexGemini-NX 80*40 mm*3 um; mobile phase: [water (0.05% NH₃H₂O+10 mMNH4HCO3)-ACN]; B %: 20%-50%, 7.8 min) to give the product (22.11 mg, 22%yield) as a solid. LCMS: Rt=0.824 min; for C₂₂H₂₄Cl₂N₆O₃ MS Calcd.:490.13; MS Found: 491.1 [M+H⁺]. ¹H NMR (400 MHz, CD₃OD) δ 7.30 (s, 2H),5.22-5.09 (m, 1H), 4.60 (t, J=7.1 Hz, 1H), 3.27-3.19 (m, 2H), 2.56-2.37(m, 2H), 2.06-1.88 (m, 3H), 1.87-1.79 (m, 1H), 1.73 (td, J=7.2, 14.0 Hz,2H), 1.60-1.44 (m, 1H), 0.96-0.75 (m, 1H), 0.54 (d, J=6.9 Hz, 2H), 0.21(dd, J=4.8, 10.4 Hz, 2H).

Example 39. Synthesis of Viral Protease Inhibitor Compound 639 and 639A

Step 1: Methyl(2S)-2-[[(2S)-2-(tert-butoxycarbonylamino)-3-cyclopropyl-propanoyl]amino]-3-[(3S)-2-oxo-3-piperidyl]propanoate

To a solution of(2S)-2-(tert-butoxycarbonylamino)-3-cyclopropyl-propanoic acid (1.07 g,4.65 mmol, 1.1 eq) and methyl(2S)-2-amino-3-[(3S)-2-oxo-3-piperidyl]propanoate (1 g, 4.22 mmol, 1 eq,HCl) in DCM (10 mL) was added DMAP (1.55 g, 12.67 mmol, 3 eq) and EDCI(1.62 g, 8.45 mmol, 2 eq). The resulting mixture was stirred at 25° C.for 1 h. Upon completion, the solution was added with H₂O (30 mL), andthen extracted with ethyl acetate (30 mL*3). The combined organic phasewas dried over Na₂SO₄, filtrated and concentrated. The residue waspurified by column chromatography (SiO₂, DCM/MeOH=30/1 to 10/1) to givemethyl(2S)-2-[[(2S)-2-(tert-butoxycarbonylamino)-3-cyclopropyl-propanoyl]amino]-3-[(3S)-2-oxo-3-piperidyl]propanoate (1.2 g, 2.92 mmol, 68.97% yield, 100% purity) was obtained asyellow oil. MS (ESI) m/z 412.3 [M+H]⁺.

Step 2:(2R)-N-(4-(tert-butyl)phenyl)-N-(2-oxo-1-(pyridin-3-yl)-2-((pyridin-4-ylmethyl)amino)ethyl)pyrrolidine-2-carboxamide

Methyl(2S)-2-[[(2S)-2-(tert-butoxycarbonylamino)-3-cyclopropyl-propanoyl]amino]-3-[(3S)-2-oxo-3-piperidyl]propanoate(600 mg, 1.46 mmol, 1 eq) in ammonia (7 M, 7.2 mL, 8.30 eq) was stirredat 50° C. for 14 h. Upon completion, the solution was concentrated togive tert-butylN-[(1S)-2-[[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxo-3-piperidyl]methyl] ethyl]amino]-1-(cyclopropylmethyl)-2-oxo-ethyl] carbamate (580 mg, crude) asyellow oil. MS (ESI) m/z 397.3 [M+H]⁺.

Step 3:(2S)-2-amino-N-[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxo-3-piperidyl]methyl]ethyl]-3-cyclopropyl-propanamide

Tert-butylN-[(1S)-2-[[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxo-3-piperidyl]methyl]ethyl]amino]-1-(cyclopropylmethyl)-2-oxo-ethyl]carbamate(580 mg, 1.46 mmol, 1 eq) in HCl/MeOH (4 M, 10.00 mL, 7.93 eq) wasstirred at 25° C. for 1 h. Upon completion, the solution wasconcentrated to give(2S)-2-amino-N-[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxo-3-piperidyl]methyl]ethyl]-3-cyclopropyl-propanamide(380 mg, crude) was obtained as yellow oil. MS (ESI) m/z 297.2 [M+H]⁺.

Step 4:(2S)-2-amino-N-[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxo-3-piperidyl]methyl]ethyl]-3-cyclopropyl-propanamide

To a solution of(2S)-2-amino-N-[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxo-3-piperidyl]methyl]ethyl]-3-cyclopropyl-propanamide(380 mg, 1.28 mmol, 1 eq) in DCM (3 mL) was added7-chloro-1H-indole-2-carboxylic acid (275.88 mg, 1.41 mmol, 1.1 eq), T3P(1.22 g, 1.93 mmol, 1.14 mL, 50% purity, 1.5 eq), and DIEA (331.44 mg,2.56 mmol, 446.68 uL, 2 eq). The mixture was stirred at 25° C. for 2 h.Upon completion, the solution was diluted with H₂O (20 mL), extractedwith DCM (30 mL*3), the combined organic phase was dried over Na₂SO₄,filtrated and concentrated. The residue was purified by prep-TLC (SiO₂,DCM:MeOH=10:1) to giveN-[(1S)-2-[[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxo-3-piperidyl]methyl]ethyl]amino]-1-(cyclopropylmethyl)-2-oxo-ethyl]-7-chloro-1H-indole-2-carboxamide(350 mg, 738.47 umol, 57.59% yield, 100% purity) as yellow oil. MS (ESI)m/z 474.3 [M+H].

Step 5: 7-chloro-N-[(1S)-2-[[(1S)-1-cyano-2-[(3S)-2-oxo-3-piperidyl]ethyl]amino]-1-(cyclopropylmethyl)-2-oxo-ethyl]-1H-indole-2-carboxamide

To a solution ofN-[(1S)-2-[[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxo-3-piperidyl]methyl]ethyl]amino]-1-(cyclopropylmethyl)-2-oxo-ethyl]-7-chloro-1H-indole-2-carboxamide(350 mg, 738.47 umol, 1 eq) in DCM (4 mL) was added Burgess reagent(527.94 mg, 2.22 mmol, 3 eq), and the solution was stirred at 25° C. for6 h. Upon completion, DCM was removed using blow dry. The residue waspurified by prep-HPLC (column: Waters Xbridge Prep OBD C18 150*40 mm*10um; mobile phase: [water (0.05% NH₃H₂O+10 mM NH₄HCO₃)-ACN]; B %:25%-55%, 8 min) to afford the product as a solid, which was furtherseparated by SFC (column: DAICEL CHIRALPAK AS (250 mm*30 mm, 10 um);mobile phase: [0.1% NH₃H₂O ETOH]; B %: 33%-33%, 8 min) to give:

7-chloro-N-[(1S)-2-[[(1S)-1-cyano-2-[(3S)-2-oxo-3-piperidyl]ethyl]amino]-1-(cyclopropylmethyl)-2-oxo-ethyl]-1H-indole-2-carboxamide(250 mg, 530.89 umol, 74.25% yield, 96.82% purity) as a solid. MS (ESI)m/z 456.2 [M+H]⁺. ¹H NMR (400 MHz, METHANOL-d₄) δ=7.58 (d, J=7.9 Hz,1H), 7.35-7.20 (m, 2H), 7.06 (t, J=7.8 Hz, 1H), 5.22-5.05 (m, 1H), 4.57(t, J=7.5 Hz, 1H), 3.27-3.14 (m, 2H), 2.61-2.34 (m, 2H), 2.09-1.61 (m,6H), 1.59-1.43 (m, 1H), 0.98-0.76 (m, 1H), 0.55 (dd, J=1.3, 8.2 Hz, 2H),0.31-0.09 (m, 2H); and

7-chloro-N-[(1R)-2-[[(1S)-1-cyano-2-[(3S)-2-oxo-3-piperidyl]ethyl]amino]-1-(cyclopropylmethyl)-2-oxo-ethyl]-1H-indole-2-carboxamide(45 mg, 98.70 umol, 13.37% yield, 100% purity) as a solid. MS (ESI) m/z456.2 [M+H]⁺. ¹H NMR (400 MHz, METHANOL-d₄) δ=7.59 (dd, J=0.9, 7.9 Hz,1H), 7.32-7.21 (m, 2H), 7.07 (t, J=7.8 Hz, 1H), 5.12-5.02 (m, 1H), 4.59(dd, J=6.4, 7.9 Hz, 1H), 3.21 (dd, J=4.6, 7.7 Hz, 2H), 2.44-2.23 (m,2H), 2.09-1.62 (m, 6H), 1.60-1.47 (m, 1H), 0.94-0.78 (m, 1H), 0.62-0.43(m, 2H), 0.27-0.11 (m, 2H).

Example 40. Synthesis of Viral Protease Inhibitor Compound 643

Step 1: Methyl(2S)-2-[[(2S)-2-(tert-butoxycarbonylamino)-4,4-dimethyl-pentanoyl]amino]-3-[(3S)-2-oxo-3-piperidyl]propanoate

T3P (2.69 g, 4.22 mmol, 2.51 mL, 50% purity, 2 eq) was added to amixture of methyl (2S)-2-amino-3-[(3S)-2-oxo-3-piperidyl]propanoate (500mg, 2.11 mmol, 1 eq, HCl),(2S)-2-(tert-butoxycarbonylamino)-4,4-dimethyl-pentanoic acid (570.0 mg,2.32 mmol, 1.1 eq) and TEA (855.0 mg, 8.45 mmol, 1.18 mL, 4 eq) in DMF(5 mL). The resulting mixture was stirred at 70° C. for 16 hr. TLC(petroleum ether: ethyl acetate=0:1/PMA) showed new spots were detected.The reaction mixture was diluted with H₂O (10 mL) and the mixture wasextracted with ethyl acetate (10 mL*3). The combined organic phase waswashed with brine (10 mL*2), dried with anhydrous Na₂SO₄, filtered andconcentrated in vacuum. The residue was purified by flash silica gelchromatography (ISCO®; 20 g SepaFlash® Silica Flash Column, Eluent of0˜100% Ethyl acetate/Petroleum ethergradient @30 mL/min). Compoundmethyl(2S)-2-[[(2S)-2-(tert-butoxycarbonylamino)-4,4-dimethyl-pentanoyl]amino]-3-[(3S)-2-oxo-3-piperidyl]propanoate(436 mg, 0.99 mmol, 47.2% yield, 97.9% purity) was obtained as a solid.

Step 2: Methyl(2S)-2-[[(2S)-2-amino-4,4-dimethyl-pentanoyl]amino]-3-[(3S)-2-oxo-3-piperidyl]propanoate

Methyl(2S)-2-[[(2S)-2-(tert-butoxycarbonylamino)-4,4-dimethyl-pentanoyl]amino]-3-[(3S)-2-oxo-3-piperidyl]propanoate(300 mg, 0.70 mmol, 1 eq) in HCl/dioxane (4 M, 175.42 uL, 1 eq) wasstirred at 25° C. for 2 hr. Compound methyl(2S)-2-[[(2S)-2-amino-4,4-dimethyl-pentanoyl]amino]-3-[(3S)-2-oxo-3-piperidyl]propanoate(250 mg, crude, HCl) was obtained as a solid and was used into next stepwithout further purification.

Step 3: Methyl(2S)-2-[[(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4,4-dimethyl-pentanoyl]amino]-3-[(3S)-2-oxo-3-piperidyl]propanoate

A mixture of methyl(2S)-2-[[(2S)-2-amino-4,4-dimethyl-pentanoyl]amino]-3-[(3S)-2-oxo-3-piperidyl]propanoate(310 mg, 0.85 mmol, 1 eq, HCl), 4-methoxy-1H-indole-2-carboxylic acid(179.1 mg, 0.93 mmol, 1.1 eq), HATU (647.8 mg, 1.70 mmol, 2 eq) andDIPEA (440.4 mg, 3.41 mmol, 0.60 mL, 4 eq) in DCM (4 mL) was stirred at25° C. for 2 hr. TLC (petroleum ether/ethyl acetate=0:1/UV 254 nm)showed new spots were detected. The reaction mixture was diluted withH₂O (10 mL) and the mixture was extracted with ethyl acetate (10 mL*3).The combined organic phase was washed with brine (10 mL*2), dried withanhydrous Na₂SO₄, filtered and concentrated in vacuum. The residue waspurified by flash silica gel chromatography (ISCO®; 12 g SepaFlash®Silica Flash Column, Eluent of 0˜100% Ethyl acetate/Petroleumethergradient @ 30 mL/min). Compound methyl(2S)-2-[[(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4,4-dimethyl-pentanoyl]amino]-3-[(3S)-2-oxo-3-piperidyl]propanoate(451 mg, 0.68 mmol, 80.1% yield) was obtained as an oil and confirmed byLC-MS.

Step 4:N-[(1S)-1-[[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxo-3-piperidyl]methyl]ethyl]carbamoyl]-3,3-dimethyl-butylJ-4-methoxy-1H-indole-2-carboxamide

NH₃ (7 M, 11.42 mL, 100 eq) was added to a mixture of methyl(2S)-2-[[(2S)-2-[(4-methoxy-1H-indole-2-carbonyl)amino]-4,4-dimethyl-pentanoyl]amino]-3-[(3S)-2-oxo-3-piperidyl]propanoate(400 mg, 0.79 mmol, 1 eq) in MeOH. Then, the mixture was stirred at 80°C. for 16 hr. TLC (DCM:MeOH=10:1/UV 254 nm) showed new spot wasdetected. The reaction mixture was concentrated in vacuum. The residuewas purified by flash silica gel chromatography (ISCO®; 12 g SepaFlash®Silica Flash Column, Eluent of 0-50% Ethyl acetate/MeOH @30 mL/min).CompoundN-[(1S)-1-[[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxo-3-piperidyl]methyl]ethyl]carbamoyl]-3,3-dimethyl-butyl]-4-methoxy-1H-indole-2-carboxamide(295 mg, 0.60 mmol, 75.1% yield, 98.9% purity) was obtained as a solid.

Step 5: N-[(1S)-1-[[(1S)-1-cyano-2-[(3S)-2-oxo-3-piperidyl]ethyl]carbamoyl]-3,3-dimethyl-butyl]-4-methoxy-1H-indole-2-carboxamide

Methoxycarbonyl-(triethylammonio)sulfonyl-azanide (284.6 mg, 1.19 mmol,2 eq) was added at the mixture ofN-[(1S)-1-[[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxo-3-piperidyl]methyl]ethyl]carbamoyl]-3,3-dimethyl-butyl]-4-methoxy-1H-indole-2-carboxamide(290 mg, 0.59 mmol, 1 eq) in DCM (3 mL) at 25° C. Then the mixture wasstirred at 25° C. for 16 hr. Thenmethoxycarbonyl-(triethylammonio)sulfonyl-azanide (142.3 mg, 0.59 mmol,1 eq) was added to the mixture and the mixture was stirred at 25° C. foranther 16 hr. The reaction mixture was diluted with H₂O (10 mL) and themixture was extracted with ethyl acetate (10 mL*3). The combined organicphase was washed with brine (10 mL*2), dried with anhydrous Na₂SO₄,filtered and concentrated in vacuum. The residue was purified byprep-HPLC (column: Welch Xtimate C18 150*25 mm*5 um; mobile phase:[water (0.05% ammonia hydroxide v/v)-MeOH]; B %: 55%-85%, 9.5 min).CompoundN-[(1S)-1-[[(1S)-1-cyano-2-[(3S)-2-oxo-3-piperidyl]ethyl]carbamoyl]-3,3-dimethyl-butyl]-4-methoxy-1H-indole-2-carboxamide(28.1 mg, 59.3 umol, 9.9% yield, 98.7% purity) was obtained as a solid.Rt=0.832 min; for C₂₅H₃₃N₅O₄ MS Calcd.: 467.25, MS Found: 468.2 [M+H⁺].¹H NMR (400 MHz, CD₃OD) δ 7.26-7.22 (m, 1H), 7.18-7.12 (m, 1H),7.05-7.00 (m, 1H), 6.51 (d, J=7.5 Hz, 1H), 5.08 (dd, J=6.3, 9.8 Hz, 1H),4.67-4.63 (m, 1H), 3.93 (s, 3H), 3.21-3.15 (m, 2H), 2.47-2.38 (m, 2H),1.98-1.72 (m, 6H), 1.70-1.58 (m, 1H), 1.54-1.43 (m, 1H), 1.02 (s, 8H),1.04-1.01 (m, 2H).

Example 41. Synthesis of Viral Protease Inhibitor Compound 681

Step 1: (2S)-methyl2-(2-(4-methoxy-1H-indole-2-carbonyl)-2-azaspiro[4.5]decane-3-carboxamido)-3-((S)-2-oxopiperidin-3-yl)propanoate

To a solution of methyl(2S)-2-amino-3-[(3S)-2-oxo-3-piperidyl]propanoate (500 mg, 2.11 mmol,1.1 eq, HCl) and2-(4-methoxy-1H-indole-2-carbonyl)-2-azaspiro[4.5]decane-3-carboxylicacid (684.45 mg, 1.92 mmol, 1 eq) in DMF (15 mL) was addedN,N-diisopropylethylamine (DIEA) (744.57 mg, 5.76 mmol, 1.00 mL, 3 eq)and (1-[bis(dimethylamino)methylene]-1H-1,2,3-triazolo[4,5-b]pyridinium3-oxide hexafluorophosphate (HATU) (730.19 mg, 1.92 mmol, 1 eq). Themixture was stirred at 20° C. for 1 h. Upon completion, the two batchreaction mixture was quenched by addition H₂O (80 mL), and extractedwith ethyl acetate (40 mL*3). The combined organic layers were washedwith brine 40 mL, dried over Na₂SO₄, filtered and concentrated underreduced pressure to get the product methyl(2S)-2-[[2-(4-methoxy-1H-indole-2-carbonyl)-2-azaspiro[4.5]decane-3-carbonyl]amino]-3-[(3S)-2-oxo-3-piperidyl]propanoate(1.35 g, crude) was obtained as white solid. MS (ESI) m/z 539.3 [M+H]⁺.

Step 2:N—((S)-1-amino-1-oxo-3-((S)-2-oxopiperidin-3-yl)propan-2-yl)-2-(4-methoxy-1H-indole-2-carbonyl)-2-azaspiro[4.5]decane-3-carboxamide

A solution of methyl(2S)-2-[[2-(4-methoxy-1H-indole-2-carbonyl)-2-azaspiro[4.5]decane-3-carbonyl]amino]-3-[(3S)-2-oxo-3-piperidyl]propanoate(650 mg. 1.21 mmol, 1 eq) in NH₃/MeOH (7 M, 3.45 mL, 20 eq) was stirredat 65° C. for 17 h. Upon completion, the two batch reaction mixture wasconcentrated under reduced pressure to get the productN-[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxo-3-piperidyl]methyl]ethyl]-2-(4-methoxy-1H-indole-2-carbonyl)-2-azaspiro[4.5]decane-3-carboxamide(1.22 g, crude) as colorless oil. MS (ESI) m/z 524.3 [M+H]⁺.

Step 3:N—((S)-1-cyano-2-((S)-2-oxopiperidin-3-yl)ethyl)-2-(4-methoxy-1H-indole-2-carbonyl)-2-azaspiro[4.5]decane-3-carboxamide

To a solution ofN-[(1S)-2-amino-2-oxo-1-[[(3S)-2-oxo-3-piperidyl]methyl]ethyl]-2-(4-methoxy-1H-indole-2-carbonyl)-2-azaspiro[4.5]decane-3-carboxamide(1.22 g, 2.33 mmol, 1 eq) in DCM (20 mL) was added Burgess reagent (1.39g, 5.82 mmol, 2.5 eq). The mixture was stirred at 20° C. for 1 h. Uponcompletion, the reaction mixture was quenched by the addition of H₂O (3mL) and then concentrated under reduced pressure to give a residue. Theresidue was purified by prep-HPLC (column: Agela DuraShell C18 250*70mm*10 um; mobile phase: [water (10 mM NH₄HCO₃)-ACN]; B %: 43%-63%, 20min) to give desired compound (490 mg) as a solid, which was furtherseparated by SFC (column: DAICEL CHIRALPAK AD (250 mm*30 mm, 10 um);mobile phase: [0.1% NH₃H₂O IPA]; B %: 58%-58%, 10 min) to afford theproductN-[(1S)-1-cyano-2-[(3S)-2-oxo-3-piperidyl]ethyl]-2-(4-methoxy-1H-indole-2-carbonyl)-2-azaspiro[4.5]decane-3-carboxamide,Isomer 1 (201.77 mg, 394.36 umol, 16.93% yield) was obtained as whitesolid. MS (ESI) m/z 506.3[M+H]⁺. ¹H NMR (400 MHz, DMSO-d₆) δ ppm 11.26(br s, 1H) 8.50-8.85 (m, 1H) 7.23 (br s, 1H) 7.00-7.16 (m, 2H) 6.89 (brs, 1H) 6.52 (br d, J=7.46 Hz, 1H) 4.86-5.06 (m, 1H) 4.48-4.79 (m, 1H)3.80-3.98 (m, 4H) 3.59 (br d, J=4.65 Hz, 1H) 3.09 (br s, 2H) 2.15-2.31(m, 3H) 1.73-2.01 (m, 2H) 1.67 (br dd, J=12.17, 8.62 Hz, 2H) 1.33-1.61(m, 12H); and

N-[(1S)-1-cyano-2-[(3S)-2-oxo-3-piperidyl]ethyl]-2-(4-methoxy-1H-indole-2-carbonyl)-2-azaspiro[4.5]decane-3-carboxamide,Isomer 2 (200.95 mg, 394.35 umol, 16.93% yield) was obtained as whitesolid. MS (ESI) m/z 506.3[M+H]⁺. ¹H NMR (400 MHz, DMSO-d₆) δ ppm 11.27(br s, 1H) 8.61 (br d, J=1.22 Hz, 1H) 7.02-7.26 (m, 3H) 6.91 (br s, 1H)6.53 (d, J=7.46 Hz, 1H) 4.91-5.06 (m, 1H) 4.62 (br s, 1H) 3.82-3.98 (m,4H) 3.52-3.75 (m, 1H) 3.09 (br s, 2H) 2.09-2.28 (m, 3H) 1.63-1.92 (m,4H) 1.33-1.62 (m, 12H).

Example 42. Synthesis of Viral Protease Inhibitor Compound 721

Step 1:(S)-methyl2-((S)-2-((tert-butoxycarbonyl)amino)-4,4-dimethylpentanamido)-3-((S)-2-oxopiperidin-3-yl)propanoate

To a solution of(2S)-2-(tert-butoxycarbonylamino)-4,4-dimethyl-pentanoic acid (2.49 g,10.14 mmol, 1.2 eq) and methyl (2S)-2-amino-3-[(3S)-2-oxo-3-piperidyl]propanoate (2 g, 8.45 mmol, 1 eq, HCl) in DCM (60 mL) was added DMAP(3.10 g, 25.35 mmol, 3 eq). Then, EDCI (3.24 g, 16.90 mmol, 2 eq) wasadded, and the resulting mixture was stirred at 25° C. for 1 h. Upon thereaction complement, the mixture was quenched by water (400 mL),extracted with DCM (150 mL*3), and then was dried by sat. NaCl (50 mL).The resulting solution was concentrated in vacuum and was purified bycolumn (SiO₂, petroleum ether:ethyl acetate=2:1 to 0:1). The resultingresidue was washed with HCl (1 M, 150 mL), extracted with DCM (50 mL*3),and then the pH of the solution was adjust pH=˜8 with sat. NaHCO₃ (30mL). The resulting mixture was extracted with DCM (100 mL), and thenconcentrated under vacuum to afford (S)-methyl2-((S)-2-((tert-butoxycarbonyl)amino)-4,4-dimethylpentanamido)-3-((S)-2-oxopiperidin-3-yl)propanoate (3 g, 6.32 mmol, 74.74% yield) as a solid. ¹H NMR (400 MHz,CDCl₃-d) δ ppm 7.61 (d, J=7.0 Hz, 1H), 6.85-6.51 (m, 1H), 6.22 (s, 1H),5.06-4.85 (m, 1H), 4.63-4.47 (m, 1H), 4.30-4.02 (m, 1H), 3.79-3.66 (m,3H), 3.35-3.25 (m, 2H), 2.42-2.24 (m, 1H), 2.14-2.05 (m, 1H), 1.96-1.66(m, 4H), 1.63-1.52 (m, 1H), 1.43 (s, 9H), 1.03-0.90 (m, 9H).

Step 2: (S)-methyl2-((S)-2-amino-4,4-dimethylpentanamido)-3-((S)-2-oxopiperidin-3-yl)propanoate

A solution of (S)-methyl 2-((S)-2-((tert-butoxycarbonyl)amino)-4,4-dimethylpentanamido)-3-((S)-2-oxopiperidin-3-yl) propanoate(1.5 g, 3.51 mmol, 1 eq) in HCl/MeOH (4 M, 20 mL) was stirred at 25° C.for 1 h. Upon the reaction complement, the mixture was concentratedunder vacuum to obtain (S)-methyl2-((S)-2-amino-4,4-dimethylpentanamido)-3-((S)-2-oxopiperidin-3-yl)propanoate(1.1 g, crude, HCl) as a solid. ¹H NMR (400 MHz, D₂O) δ ppm 4.57 (dd,J=4.8, 10.3 Hz, 1H), 3.98 (dd, J=5.2, 7.8 Hz, 1H), 3.78-3.65 (m, 3H),3.29-3.14 (m, 2H), 2.75-2.33 (m, 1H), 2.24-1.47 (m, 8H), 1.04-0.86 (m,9H).

Step 3:(S)-methyl2-((S)-2-(7-chloro-1H-indole-2-carboxamido)-4,4-dimethylpentanamido)-3-((S)-2-oxopiperidin-3-yl)propanoate

To a solution of (S)-methyl2-((S)-2-amino-4,4-dimethylpentanamido)-3-((S)-2-oxopiperidin-3-yl)propanoate(550 mg*2, HCl salt, 1.68 mmol, 1 eq) and7-chloro-1H-indole-2-carboxylic acid (394.29 mg, 2.02 mmol, 1.2 eq) inDCM (6 mL) was added DMAP (615.66 mg, 5.04 mmol, 3 eq). EDCI (644.05 mg,3.36 mmol, 2 eq) was added to the mixture at 25° C., and the mixture wasstirred at 25° C. for 1 h. Upon the reaction complement, the mixture wasquenched by water (200 mL), extracted with DCM (70 mL*3), and thenconcentrated under vacuum. The resulting residue was purified by column(SiO₂, petroleum ether: ethyl acetate=1:1 to 0:1), concentrated invacuum, and then was washed with 1M HCl (100 mL) and extracted with DCM(30 mL*3). The organic phase was adjusted to pH=˜7 with sat. NaHCO₃ (30mL), and then concentrated in vacuum to obtain (S)-methyl2-((S)-2-(7-chloro-1H-indole-2-carboxamido)-4,4-dimethylpentanamido)-3-((S)-2-oxopiperidin-3-yl)propanoate(650 mg, 1.16 mmol, 40% yield) as a solid. MS (ESI) m/z 505.2 [M+H]⁺; ¹HNMR (400 MHz, MeOD-d₄) δ ppm 7.58 (d, J=7.8 Hz, 1H), 7.32-7.17 (m, 2H),7.06 (t, J=7.8 Hz, 1H), 4.73 (dd, J=3.8, 8.6 Hz, 1H), 4.55 (dd, J=4.0,11.7 Hz, 1H), 3.71 (s, 3H), 3.35 (s, 1H), 3.24-3.01 (m, 2H), 2.49-2.22(m, 2H), 2.02-1.40 (m, 8H), 1.08-0.96 (m, 9H).

Step 4:N—((S)-1-(((S)-1-amino-1-oxo-3-((S)-2-oxopiperidin-3-yl)propan-2-yl)amino)-4,4-dimethyl-1-oxopentan-2-yl)-7-chloro-1H-indole-2-carboxamide

A solution of (S)-methyl2-((S)-2-(7-chloro-1H-indole-2-carboxamido)-4,4-dimethylpentanamido)-3-((S)-2-oxopiperidin-3-yl)propanoate(650 mg, 1.29 mmol, 1 eq) in NH₃/MeOH (7M, 10 mL) was stirred at 50° C.for 16 h. Upon the reaction complement, the mixture was concentrated invacuum to obtainN—((S)-1-(((S)-1-amino-1-oxo-3-((S)-2-oxopiperidin-3-yl) propan-2-yl)amino)-4,4-dimethyl-1-oxopentan-2-yl)-7-chloro-1H-indole-2-carboxamide(450 mg, crude) as a light yellow solid. MS (ESI) m/z 490.3 [M+H]⁺

Step 5:7-chloro-N—((S)-1-(((S)-1-cyano-2-((S)-2-oxopiperidin-3-yl)ethyl)amino)-4,4-dimethyl-1-oxopentan-2-yl)-1H-indole-2-carboxamide

To a solution ofN—((S)-1-(((S)-1-amino-1-oxo-3-((S)-2-oxopiperidin-3-yl) propan-2-yl)amino)-4,4-dimethyl-1-oxopentan-2-yl)-7-chloro-1H-indole-2-carboxamide(430 mg, 877.56 umol, 1 eq) in DCM (10 mL) was added Burgess reagent(627.38 mg, 2.63 mmol, 3 eq). The reaction mixture was stirred at 25° C.for 4 h. Upon the reaction complement, the mixture was quenched by water(10 mL), dried with a stream of N₂ and purified by prep-HPLC (column:Kromasil C18 (250*50 mm*10 um); mobile phase: [water (10 mMNH₄HCO₃)-ACN]; B %: 35%-65%, 10 min) to obtain7-chloro-N—((S)-1-(((S)-1-cyano-2-((S)-2-oxopiperidin-3-yl)ethyl)amino)-4,4-dimethyl-1-oxopentan-2-yl)-1H-indole-2-carboxamide(205 mg, 424.79 umol, 48.41% yield) as a white solid. MS (ESI) m/z 472.2[M+H]⁺; 1H NMR (400 MHz, DMSO-d₆) δ ppm 11.70 (s, 1H), 9.02 (d, J=8.0Hz, 1H), 8.71 (d, J=8.0 Hz, 1H), 7.63 (d, J=8.0 Hz, 1H), 7.52 (s, 1H),7.34-7.23 (m, 2H), 7.07 (t, J=7.8 Hz, 1H), 5.05 (q, J=8.2 Hz, 1H),4.63-4.54 (m, 1H), 3.07 (s, 2H), 2.30-2.18 (m, 2H), 1.88-1.32 (m, 7H),0.95 (s, 9H).

Example 43. Evaluation of Antiviral Activity of Compounds AgainstCOVID-19 (nCoV-2019, SARS-CoV2) Mpro in the Enzymatic Assay

Compounds were assayed using standard methods to assess compoundactivity and IC50. As an exemplary for assessment of the SARS-COV2 Mpro,the C-His6-tagged Mpro (NC_045512) was cloned, expressed in E. coli andpurified. The assay buffer contained 20 mM of Tris-HCl (pH 7.3), 100 mMof NaCl, 1 mM of EDTA, 5 mM of TCEP and 0.1% BSA. The finalconcentrations of the Mpro protein and substrate were 25 nM and 25 μM,respectively, in the Mpro enzymatic assay. The Km of the Mpro substratefor the protease was 13.5 μM.

The compounds were added to an assay plate. For 100% inhibition control(HPE, hundred percent effect), 1 μM GC376 was added. For no inhibitioncontrol (ZPE, zero percent effect), no compound was added. Each activitytesting point had a relevant background control to normalize thefluorescence interference of compound.

IC50 values of compounds were calculated with the GraphPad Prismsoftware using the nonlinear regression model of log(inhibitor) vs.response—Variable slope (four parameters). The inhibition activity wascalculated using the formula below, IC50 values was calculated using theInhibition % data.

Inhibition %=[(Sample−Average ZPE)/(Average HPE−AverageZPE)]*100%^(##)HEP: Hundred percent effect controls. Containingsubstrate+enzyme+1 μM GC376. ZPE: Zero percent effective controls.Containing enzyme+substrate, no compound. Sample: Compound activitytesting wells. Containing compound+enzyme+substrate. BG: Compoundbackground control wells. Containing compound+substrate, no enzyme.

Example 44. Evaluation of Antiviral Activity of Compounds Against HumanCoronavirus (HCov) 229E and OC43 in the Cytopathic Effect (CPE) Assays

Compounds were assayed using standard methods against multiplecoronaviral strains, including HCoV 229E and OC43 strains. The antiviralactivity of compounds was calculated based on the protection of thevirus-induced CPE at each concentration normalized by the virus control.

Reagents and instruments used in this assay include luminescent cellviability assay kit CellTiter Glo (Promega) and Microplate ReaderSynergy2 (BioTek).

Virus —HCoV 229E

Cytopathic effect (CPE) was measured by CellTiter Glo following themanufacturer's manual. The antiviral activity of compounds wascalculated based on the protection of the virus-induced CPE at eachconcentration normalized by the virus control.

Virus —HCov OC43

Reference compound used was remdesivir; detection reagent: CellTiterGlo.) The CPE were measured by CellTiter Glo following themanufacturer's manual. The antiviral activity of compounds wascalculated based on the protection of the virus-induced CPE at eachconcentration normalized by the virus control.

The cytotoxicity of compounds was assessed under the same conditions,but without virus infection, in parallel. Cell viability was measuredwith CellTiter Glo. The antiviral activity and cytotoxicity of compoundswere expressed as % Inhibition and % Viability, respectively, andcalculated with formulas.

Table 2, Table 3 and Table 4 below show activity data.

TABLE 2 Activity data for compounds. Sars 229E CoV2 mPRO mPRO IC50 IC50Compound No. (μM) (μM) 101 D D 103 D D 127 B C 129 C D 131 D D 133 D D134 D D 134 (Isomer 1) D D 134 (Isomer 2) D D 135 D D 135 (Isomer 1) C C135 (Isomer 2) D D 136 D D 143 C C 145 D D 147 A D 149 C D 153 B D 165 AB 167 C C 171 D D 183 C D 185 D D 197 D D 201 C C 205 D D 209 B C 213 AB 223 (Isomer 1) B B 223 (Isomer 2) A A 225 A A 227 A C 231 A A 237 A A241 A A 245 A C 249 A A 253 C C 265 C C 267 A A 267A D D 269 A A 269 A A271 A A 271A (Isomer 1) A A 271A (Isomer 2) A A 271A (Isomer 3) A A 271A(Isomer 4) A A 273A A A 273B A A 273C C A 279 A A 305 D D 323 (Isomer 1)D D 323 (Isomer 2) D D 325 B B 327 D D 329 D D 331 (Isomer 1) D D 331(Isomer 2) D D 344D D D 344C D D 344A D D 345 D D 345 (Isomer 1) D D 345(Isomer 2) D D 355 C D 357 A B 359 B C 361 D D 363 D D 365 (Isomer 1) CD 365 (Isomer 2) C B 369 (Isomer 1) B B 369 (Isomer 2) C C 375A D D 377D D 379 D D 383 C C 385 (Isomer 1) D D 385 (Isomer 2) D C 387 A B 389A(Isomer 1) D D 391 A A 393 D D 395 (Isomer 1) D D 395 (Isomer 2) D D 397D D 399 (Isomer 1) D D 401 D D 401 (Isomer 1) D D 401 (Isomer 2) C C 405D D 407 D C 433 D D 439 A B 449 B B 449 (Isomer 1) A A 449 (Isomer 2) BC 451 (Isomer 1) A A 451 (Isomer 2) B C 455 A B 457 A A 459 A A 465 B B465 (Isomer 1) A A 465 (Isomer 2) B C 467 (Isomer 1) C C 469 A B 469(Isomer 1 & A A Isomer 2) 469 (Isomer 3) A A 469 (Isomer 4) A A 471 B B473 (Isomer 1) A A 473 (Isomer 2) A A 475 (Isomer 1 & C B Isomer 2) 475(Isomer 3) B A 475 (Isomer 4) A A 477 A B 479 B A 481 (Isomer 1) A A 481(Isomer 2) A A 483 A A 483 (Isomer 1) A A 483 (Isomer 2) A A 489(Isomer 1) A A 489 (Isomer 2) A A 491 D D 491 (Isomer 1) D D 491 (Isomer2) A B 491A (Isomer 1) A A 491A (Isomer 2) D D 495 (Isomer 1) A A 495(Isomer 2) A A 497 (Isomer 2) D D 499 D D 501 A A 505 A B 507 (Isomer1.1) D D 507 (Isomer 1.2) D D 507 (Isomer 2.1) D D 507 (Isomer 2.2) D D509 D D 511 D D 511 (Isomer 1) D D 511 (Isomer 2) D D 513 (Isomer 1) C C513 (Isomer 2) C D 515 D D 519 D D 531 D D 535 A C 547 (Isomer 2) D B551 D D 555 B B 577 D D 581 A B 583 A B 591 (Isomer 1) A A 591 (Isomer2) A C 595 D D 598 C D 623 A A 625 D D 635 D D 637 D D 639 (Isomer 1) DD 643 D D 649 C C 653 D D 659 A A 681 (Isomer 1) D D 711 D D 715 D D 717D D 719 (Isomer 2) D D 721 D D 723 (Isomer 2) D D 725 D D 729 (Isomer 1)D D 731 (Isomer 1) D D 733 (Isomer 1) D D 735 D D 737 D D 739 D D 743(Isomer 2) D D 745 D D 747 D D A > 30 μM, B > 10 μM and ≤30 μM, C ≥ 2 μMand ≤10 μM, D < 2 μM.

TABLE 3 Activity data for compounds. 229E CPE Compound No. EC₅₀ (μM) 101D 103 D 127 C 131 C 133 D 134 D 134 (Isomer 1) D 134 (Isomer 2) D 135 D135 (Isomer 2) D 136 A 149 C 171 D 185 D 197 D 205 D 323 (Isomer 1) D323 (Isomer 2) D 327 C 329 D 331 (Isomer 1) D 331 (Isomer 2) D 344D D344C D 344A D 345 D 345 (Isomer 1) D 345 (Isomer 2) D 355 A 361 D 363 D375A D 377 D 379 D 385 (Isomer 1) D 385 (Isomer 2) D 389A (Isomer 1) D393 D 397 D 399 (Isomer 1) D 401 D 401 (Isomer 1) D 405 D 407 D 433 C491 D 497 (Isomer 2) D 507 (Isomer 1.1) D 507 (Isomer 1.2) D 507 (Isomer2.1) D 507 (Isomer 2.2) D 509 D 511 D 511 (Isomer 1) D 511 (Isomer 2) D513 (Isomer 2) C 519 D 531 D 551 C 577 D 598 D 635 D 637 D 639(Isomer 1) D 643 D 653 D 681 (Isomer 1) D 711 D 715 D 717 D 719 (Isomer2) D 721 D 723 (Isomer 2) D 725 D 729 (Isomer 1) D 731 (Isomer 1) D 733(Isomer 1) D 735 D 737 D 739 D 743 (Isomer 2) D 745 D 747 D A > 30 μM,B > 10 μM and ≤30 μM, C ≥ 2 μM and ≤10 μM, D < 2 μM.

TABLE 4 Activity data for compounds. Compound 229E No. CC₅₀ 130(Isomer 1) A 135 A 170 A A > 30 μM, B > 10 μM and ≤30 μM, C ≥ 2 μM and≤10 μM, D < 2 μM.

INCORPORATION BY REFERENCE

All publications and patents mentioned herein, including those itemslisted below, are hereby incorporated by reference in their entirety forall purposes as if each individual publication or patent wasspecifically and individually incorporated by reference. In case ofconflict, the present application, including any definitions herein,will control.

EQUIVALENTS

While specific embodiments of the subject disclosure have beendiscussed, the above specification is illustrative and not restrictive.Many variations of the disclosure will become apparent to those skilledin the art upon review of this specification. The full scope of thedisclosure should be determined by reference to the claims, along withtheir full scope of equivalents, and the specification, along with suchvariations.

Unless otherwise indicated, all numbers expressing quantities ofingredients, reaction conditions, and so forth used in the specificationand claims are to be understood as being modified in all instances bythe term “about.” Accordingly, unless indicated to the contrary, thenumerical parameters set forth in this specification and attached claimsare approximations that may vary depending upon the desired propertiessought to be obtained by the present disclosure.

What is claimed:
 1. A compound represented by:

wherein: R^(3a) is selected from

and a 4-10 membered heterocycle; X is selected from CH, C(CH₃), and N; Ais cyano; R³ is selected from 5-10 membered heteroaryl and 4-10 memberedheterocycle; R^(3b) is selected from hydrogen and C₁-C₈alkyl; R^(1a) isselected from the group consisting of C₁-C₈alkyl, —(C₁-C₈alkyl)-R¹,—(C₁-C₈alkyl)-CN, C₃-C₁₀cycloalkyl, C₆-C₁₄aryl, 4-10 memberedheterocycle and 5-10 membered heteroaryl; R¹ is selected from the groupconsisting of C₁-C₈alkyl, C₂-C₁₀alkenyl, C₂-C₁₀alkynyl,C₃-C₁₀cycloalkyl, C₆-C₁₄aryl, 5-10 membered heteroaryl and 4-10 memberedheterocycle; R^(1b) is selected from hydrogen and C₁-C₈alkyl; R² isselected from the group consisting of —NHC(O)R^(B), —NHC(O)N(R^(B))₂,—NHC(O)C(R^(C))₂R^(B), —NHS(O)₂R^(B), 4-10 membered heterocycle,C₆-C₁₄aryl and 5-10 membered heteroaryl bound through the carbon ornitrogen atom, wherein R² may optionally be substituted by one, two, orthree substituents each selected from R^(x); R^(C) is independentlyselected, for each occurrence, from hydrogen and C₁-C₈alkyl; R^(1a) andR² may be joined together to form, together with the carbon to whichthey are attached, a 4-10 membered heterocycle or a C₃-C₁₀cycloalkyl,wherein the cycloalkyl or heterocycle may optionally be substituted byone, two or three substituents each selected from R^(A); R^(B) isindependently selected, for each occurrence, from the group consistingof C₁-C₈alkyl, C₂-C₁₀alkenyl, and C₂-C₁₀alkynyl; R^(A) is independentlyselected, for each occurrence, from the group consisting of halogen,cyano, hydroxyl, oxo, SF₅, —NH₂, —O-phenyl, —O—(C₁-C₈alkyl)-phenyl,—C(O)-(5-10 membered heteroaryl), —C(O)-(4-10 membered heterocycle),—C(O)—O-(4-10 membered heterocycle), —C(O)—OC(CH₃)₃,—C(O)—(C₂-C₁₀alkenyl)-(C₆-C₁₄aryl), C₁-C₈alkyl, C₂-C₁₀alkenyl,C₂-C₁₀alkynyl, C₁-C₈heteroalkyl, C₁-C₈alkoxy, C₃-C₁₀cycloalkyl,—(C₁-C₈alkyl)-(C₆-C₁₄aryl), —(C₁-C₈alkyl)-(5-10 membered heteroaryl),C₆-C₁₄aryl, 5-10 membered heteroaryl and 4-10 membered heterocycle;R^(x) is independently selected, for each occurrence, from the groupconsisting of halogen, hydroxyl, oxo, SF₅, cyano, —C(O)O(CH₃),—N(R^(y))₂, —N(R^(y))C(O)R^(y), C₁-C₈alkyl, C₁-C₈alkoxy,C₃-C₁₀cycloalkyl, C₆-C₁₄aryl, 5-10 membered heteroaryl and 4-10 memberedheterocycle; and R^(y) is independently selected, for each occurrence,from the group consisting of hydrogen, C₁-C₈alkyl, C₁-C₈alkoxy,—(C₁-C₈alkoxy)-(5-10 membered aryl) and C₃-C₆cycloalkyl.
 2. A compoundrepresented by:

wherein R^(1a) is selected from the group consisting of C₁-C₈alkyl,—(C₁-C₈alkyl)-R¹, —(C₁-C₈alkyl)-CN, C₃-C₁₀cycloalkyl, C₆-C₁₄aryl, 4-10membered heterocycle and 5-10 membered heteroaryl; R¹ is selected fromthe group consisting of C₁-C₈alkyl, C₂-C₁₀alkenyl, C₂-C₁₀alkynyl,C₃-C₁₀cycloalkyl, C₆-C₁₄aryl, 5-10 membered heteroaryl and 4-10 memberedheterocycle, wherein R¹ may optionally be substituted by one, two, orthree substituents each selected from R^(A); R^(1b) is selected fromhydrogen and C₁-C₈alkyl; R² is selected from the group consisting of—NHC(O)R^(B), —NHC(O)N(R^(B))₂, —NHC(O)C(R^(C))₂R^(B), —NHS(O)₂R^(B),4-10 membered heterocycle, C₆-C₁₄aryl and 5-10 membered heteroaryl boundthrough the carbon or nitrogen atom, wherein R² may optionally besubstituted by one, two, or three substituents each selected from R^(x);R^(C) is independently selected, for each occurrence, from hydrogen andC₁-C₈alkyl; R^(1a) and R² may be joined together to form, together withthe carbon to which they are attached, a 4-10 membered heterocycle or aC₃-C₁₀cycloalkyl, wherein the cycloalkyl or heterocycle may optionallybe substituted by one, two or three substituents each selected fromR^(A); R^(B) is independently selected, for each occurrence, from thegroup consisting of C₁-C₈alkyl, C₂-C₁₀alkenyl, and C₂-C₁₀alkynyl, R^(A)is independently selected, for each occurrence, from the groupconsisting of halogen, cyano, hydroxyl, oxo, SF₅, —NH₂, —O-phenyl,—O—(C₁-C₈alkyl)-phenyl, —C(O)-(5-10 membered heteroaryl), —C(O)-(4-10membered heterocycle), —C(O)—O-(4-10 membered heterocycle),—C(O)—OC(CH₃)₃, —C(O)—(C₂-C₁₀alkenyl)-(C₆-C₁₄aryl), C₁-C₈alkyl,C₂-C₁₀alkenyl, C₂-C₁₀alkynyl, C₁-C₈heteroalkyl, C₁-C₈alkoxy,C₃-C₁₀cycloalkyl, —(C₁-C₈alkyl)-(C₆-C₁₄aryl), —(C₁-C₈alkyl)-(5-10membered heteroaryl), C₆-C₁₄aryl, 5-10 membered heteroaryl and 4-10membered heterocycle; R^(x) is independently selected, for eachoccurrence, from the group consisting of halogen, hydroxyl, oxo, SF₅,cyano, —C(O)O(CH₃), —N(R^(y))₂, —N(R^(y))C(O)R^(y), C₁-C₈alkyl,C₁-C₈alkoxy, C₃-C₁₀cycloalkyl, C₆-C₁₄aryl, 5-10 membered heteroaryl and4-10 membered heterocycle; and R^(y) is independently selected, for eachoccurrence, from the group consisting of hydrogen, C₁-C₈alkyl,C₁-C₈alkoxy, —(C₁-C₈alkoxy)-(5-10 membered aryl) and C₃-C₆cycloalkyl.